From 8ebefab1d70c12f0eefde97d448a9c0e40672368 Mon Sep 17 00:00:00 2001
From: Saskia Hiltemann <saskia.hiltemann@pharmazie.uni-freiburg.de>
Date: Wed, 11 Oct 2023 15:30:17 +0200
Subject: [PATCH] add code
---
...ur_methods_noiseqbio_hoecker_20210527.html | 1064 +++++++++++++++++
...aseqhoecker 3d_pca_plot_hoecker_20210527.r | 308 +++++
2 files changed, 1372 insertions(+)
create mode 100644 workflows/personal haasf 2021 madland new_deg_pipe_four_methods_noiseqbio_hoecker_20210527.html
create mode 100644 workflows/personal haasf 2021 madland rnaseqhoecker 3d_pca_plot_hoecker_20210527.r
diff --git a/workflows/personal haasf 2021 madland new_deg_pipe_four_methods_noiseqbio_hoecker_20210527.html b/workflows/personal haasf 2021 madland new_deg_pipe_four_methods_noiseqbio_hoecker_20210527.html
new file mode 100644
index 0000000..0a44557
--- /dev/null
+++ b/workflows/personal haasf 2021 madland new_deg_pipe_four_methods_noiseqbio_hoecker_20210527.html
@@ -0,0 +1,1064 @@
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+ <dl class="code">
+<dt><a href="/lab/wiki/_export/code/personal:haasf:2021:madland:new_deg_pipe_four_methods_noiseqbio_hoecker_20210527?codeblock=0" title="Download Snippet" class="mediafile mf_r">:personal:haasf:2021:madland:new_deg_pipe_four_methods_noiseqbio_hoecker_20210527.r</a></dt>
+<dd><pre class="code rsplus"><span class="co1">###############################################################</span>
+<span class="co1">## DEG pipeline with edgeR, DESeq2 and NOISeq #</span>
+<span class="co1">## Modified from the template of Dr. Kristian Ullrich 2014 #</span>
+<span class="co1">## @fabianhaas, AG Rensing, Marburg, Jan 2016 #</span>
+<span class="co1">###############################################################</span>
+<span class="co1"># The pipeline expects sample triplicates.</span>
+<span class="co1"># If you don't have three samples of one condition, use face files with zero counts.</span>
+<span class="co1"># RPKM calculation is optional.</span>
+<span class="co1"># Additional program to sum up the tsv files: /mnt/nas_temp/home/haasf/Program/sumup_htseq_counts.pl folder file_prefix</span>
+
+<span class="co1">###########################################</span>
+<span class="co1">## please define your variables #</span>
+<span class="co1">###########################################</span>
+
+saveat <span class="sy0"><-</span> <span class="st0">"/mnt/NAS_coruscant_datashare/haasf/madland_RNA-seq_Hoecker/DEGs_0.9"</span>
+
+<a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/file.html"><span class="kw2">file</span></a> <span class="sy0"><-</span> <span class="st0">'/mnt/NAS_coruscant_datashare/haasf/madland_RNA-seq_Hoecker/31315.p.sort.counts'</span>
+
+<span class="co1"># Table with the length and the GC content</span>
+LenGCTable <span class="sy0"><-</span> <span class="st0">"/mnt/NAS_coruscant_datashare/haasf/GeneAtlas_RNASeq/DEG_2nd_round/cosmoss_V3.3.release_2016-07-22.IsoformV31.fasta.length_GC_Contig_Daten_for_34840_1nd.csv"</span>
+
+<span class="co1"># Column position of the gene name and the width/gc content (first column is gene name!)</span>
+myLenPos <span class="sy0"><-</span> <span class="nu0">1</span>
+myGCPos <span class="sy0"><-</span> <span class="nu0">2</span>
+
+<span class="co1"># </span>
+<span class="co1"># hoo <- c("","")</span>
+<span class="co1"># sampleLists <- c()</span>
+<span class="co1"># for(a in hoo) {</span>
+<span class="co1"># for(b in hoo) {</span>
+<span class="co1"># if(a!=b) {</span>
+<span class="co1"># tmp <- c(a,b)</span>
+<span class="co1"># sampleLists <- c(sampleLists, list(tmp))</span>
+<span class="co1"># }</span>
+<span class="co1"># }</span>
+<span class="co1"># }</span>
+
+
+sampleLists <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/list.html"><span class="kw2">list</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span><span class="st0">"cop_D"</span>, <span class="st0">"cop_L"</span><span class="br0">)</span>,
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span><span class="st0">"cop_D"</span>, <span class="st0">"spa_D"</span><span class="br0">)</span>,
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span><span class="st0">"cop_D"</span>, <span class="st0">"spa_L"</span><span class="br0">)</span>,
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span><span class="st0">"cop_D"</span>, <span class="st0">"WT_D"</span><span class="br0">)</span>,
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span><span class="st0">"cop_D"</span>, <span class="st0">"WT_L"</span><span class="br0">)</span>,
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span><span class="st0">"cop_L"</span>, <span class="st0">"spa_D"</span><span class="br0">)</span>,
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span><span class="st0">"cop_L"</span>, <span class="st0">"spa_L"</span><span class="br0">)</span>,
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span><span class="st0">"cop_L"</span>, <span class="st0">"WT_D"</span><span class="br0">)</span>,
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span><span class="st0">"cop_L"</span>, <span class="st0">"WT_L"</span><span class="br0">)</span>,
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span><span class="st0">"spa_D"</span>, <span class="st0">"spa_L"</span><span class="br0">)</span>,
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span><span class="st0">"spa_D"</span>, <span class="st0">"WT_D"</span><span class="br0">)</span>,
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span><span class="st0">"spa_D"</span>, <span class="st0">"WT_L"</span><span class="br0">)</span>,
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span><span class="st0">"spa_L"</span>, <span class="st0">"WT_D"</span><span class="br0">)</span>,
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span><span class="st0">"spa_L"</span>, <span class="st0">"WT_L"</span><span class="br0">)</span>,
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span><span class="st0">"WT_D"</span>, <span class="st0">"WT_L"</span><span class="br0">)</span>
+ <span class="br0">)</span>
+
+
+<span class="co1"># Do you want a RPKM value table (1/0)</span>
+<span class="co1"># Be warned, it takes a while to do this. approx. 10 minutes for 35000 genes and 6 samples.</span>
+rpkm <span class="sy0"><-</span> <span class="nu0">0</span>
+<span class="co1"># Are the data original HTSeq files? yes <- 1 ; no <- 0</span>
+htseq <span class="sy0"><-</span> <span class="nu0">0</span>
+
+<span class="co1"># threshold settings for the R packages</span>
+<span class="co1">#edgeR</span>
+pvtedgeR <span class="sy0"><-</span> <span class="nu0">0.001</span>
+<span class="co1">#DESeq2</span>
+pvtDESeq2 <span class="sy0"><-</span> <span class="nu0">0.001</span>
+<span class="co1">#NOISeq</span>
+pvtNOISeq <span class="sy0"><-</span> <span class="nu0">0.9</span>
+
+<span class="co1"># Output folder names</span>
+edgeRDir <span class="sy0"><-</span> <span class="st0">"edgeR"</span>
+DESeq2Dir <span class="sy0"><-</span> <span class="st0">"DESeq2"</span>
+NOISeqDir <span class="sy0"><-</span> <span class="st0">"NOISeq"</span>
+
+<span class="co1">#########################</span>
+<span class="co1">## stop editing here!! ##</span>
+<span class="co1">#########################</span>
+
+
+<span class="co1">###########################################</span>
+<span class="co1">## executiv function #</span>
+<span class="co1">###########################################</span>
+
+workflow <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/function.html"><span class="kw2">function</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/file.html"><span class="kw2">file</span></a>, saveat, SampleNames, LenGCTable, myLenPos, myGCPos, rpkm, pvtedgeR, pvtDESeq2, pvtNOISeq, edgeRDir, DESeq2Dir, NOISeqDir, htseq<span class="br0">)</span>
+<span class="br0">{</span>
+ <span class="co1"># setwd(workingFolder) # set workspace</span>
+
+ sampleNameI <span class="sy0"><-</span> SampleNames<span class="br0">[</span><span class="nu0">1</span><span class="br0">]</span>
+ sampleNameII <span class="sy0"><-</span> SampleNames<span class="br0">[</span><span class="nu0">2</span><span class="br0">]</span>
+
+ <span class="co1"># Comparison name</span>
+ cName <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/paste.html"><span class="kw2">paste</span></a><span class="br0">(</span>sampleNameI, sampleNameII, sep <span class="sy0">=</span> <span class="st0">" vs. "</span><span class="br0">)</span>
+
+ filename <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/strsplit.html"><span class="kw2">strsplit</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/file.html"><span class="kw2">file</span></a>, <span class="st0">"/"</span><span class="br0">)</span>
+ filename <span class="sy0"><-</span> filename<span class="br0">[</span><span class="br0">[</span><span class="nu0">1</span><span class="br0">]</span><span class="br0">]</span><span class="br0">[</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/length.html"><span class="kw2">length</span></a><span class="br0">(</span>filename<span class="br0">[</span><span class="br0">[</span><span class="nu0">1</span><span class="br0">]</span><span class="br0">]</span><span class="br0">)</span><span class="br0">]</span> <span class="co1"># long but it's working</span>
+ sampleName <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/gsub.html"><span class="kw2">gsub</span></a><span class="br0">(</span><span class="st0">", "</span>,<span class="st0">"_"</span>,<a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/toString.html"><span class="kw2">toString</span></a><span class="br0">(</span>SampleNames<span class="br0">)</span><span class="br0">)</span>
+ samples <span class="sy0"><-</span> SampleNames
+ <span class="co1"># create output dir</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/dir.create.html"><span class="kw2">dir.<span class="me1">create</span></span></a><span class="br0">(</span>saveat, showWarnings <span class="sy0">=</span> FALSE<span class="br0">)</span>
+ outdir <span class="sy0"><-</span> paste0<span class="br0">(</span>saveat,<span class="st0">"/"</span>,sampleName<span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/dir.create.html"><span class="kw2">dir.<span class="me1">create</span></span></a><span class="br0">(</span>outdir<span class="br0">)</span>
+
+ <span class="co1"># Start the log file</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/sink.html"><span class="kw2">sink</span></a><span class="br0">(</span>paste0<span class="br0">(</span>outdir, <span class="st0">"/DEGpipe_"</span>,cName, <span class="st0">".log"</span><span class="br0">)</span><span class="br0">)</span>
+
+ <span class="co1"># print parameter into the log file</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span><span class="st0">"set parameters:"</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span>paste0<span class="br0">(</span><span class="st0">"Counts file:"</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/file.html"><span class="kw2">file</span></a><span class="br0">)</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span>paste0<span class="br0">(</span><span class="st0">"Results stored at:"</span>, saveat<span class="br0">)</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span>paste0<span class="br0">(</span><span class="st0">"SampleNames: "</span>,SampleNames<span class="br0">)</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span>paste0<span class="br0">(</span><span class="st0">"LenGCTable: "</span>,LenGCTable<span class="br0">)</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span>paste0<span class="br0">(</span><span class="st0">"myLenPos: "</span>,myLenPos<span class="br0">)</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span>paste0<span class="br0">(</span><span class="st0">"myGCPos: "</span>,myGCPos<span class="br0">)</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span>paste0<span class="br0">(</span><span class="st0">"rpkm: "</span>,rpkm<span class="br0">)</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span>paste0<span class="br0">(</span><span class="st0">"htseq: "</span>,htseq<span class="br0">)</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span>paste0<span class="br0">(</span><span class="st0">"pvtedgeR: "</span>,pvtedgeR<span class="br0">)</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span>paste0<span class="br0">(</span><span class="st0">"pvtDESeq2: "</span>,pvtDESeq2<span class="br0">)</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span>paste0<span class="br0">(</span><span class="st0">"pvtNOISeq: "</span>,pvtNOISeq<span class="br0">)</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span>paste0<span class="br0">(</span><span class="st0">"edgeRDir: "</span>,edgeRDir<span class="br0">)</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span>paste0<span class="br0">(</span><span class="st0">"DESeq2Dir: "</span>,DESeq2Dir<span class="br0">)</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span>paste0<span class="br0">(</span><span class="st0">"NOISeqDir: "</span>,NOISeqDir<span class="br0">)</span><span class="br0">)</span>
+ <span class="co1"># session and package infos for the log file</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/sessionInfo.html"><span class="kw8">sessionInfo</span></a><span class="br0">(</span><span class="br0">)</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/Sys.info.html"><span class="kw2">Sys.<span class="me1">info</span></span></a><span class="br0">(</span><span class="br0">)</span><span class="br0">)</span>
+
+ <span class="co1"># load spike-in count tables</span>
+ data0 <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/read.table.html"><span class="kw8">read.<span class="me1">table</span></span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/file.html"><span class="kw2">file</span></a>, header<span class="sy0">=</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/T.html"><span class="kw2">T</span></a>, sep<span class="sy0">=</span><span class="st0">"<span class="es0">\t</span>"</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/row.names.html"><span class="kw2">row.<span class="me1">names</span></span></a><span class="sy0">=</span><span class="nu0">1</span><span class="br0">)</span>
+ <span class="co1"># just if the gene ids not ending with .1 (it is nessessery for NOISeqbio iteration step)</span>
+ <span class="co1">#row.names(data0) <- paste0(row.names(data0), ".1")</span>
+
+ <span class="co1"># remove HTSeq rows like "__no_feature"</span>
+ data0 <span class="sy0"><-</span> data0<span class="br0">[</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/with.html"><span class="kw2">with</span></a><span class="br0">(</span>data0, <span class="sy0">!</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/grepl.html"><span class="kw2">grepl</span></a><span class="br0">(</span><span class="st0">'__'</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/rownames.html"><span class="kw2">rownames</span></a><span class="br0">(</span>data0<span class="br0">)</span><span class="br0">)</span><span class="br0">)</span> , <span class="br0">]</span>
+ data0 <span class="sy0"><-</span> data0<span class="br0">[</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/with.html"><span class="kw2">with</span></a><span class="br0">(</span>data0, <span class="sy0">!</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/grepl.html"><span class="kw2">grepl</span></a><span class="br0">(</span><span class="st0">'ERCC'</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/rownames.html"><span class="kw2">rownames</span></a><span class="br0">(</span>data0<span class="br0">)</span><span class="br0">)</span><span class="br0">)</span> , <span class="br0">]</span>
+ <span class="co1">#data0 <- data0[ , with(data0, !grepl('X.1', colnames(data0)))]</span>
+ <span class="co1">#rename col names (library name to roman number)</span>
+
+ <span class="co1"># librariesName <- c("56754_WT_Naturally_3.bam.sort.fastq.unmapped.sam.sort.bam", "56753_WT_Naturally_2.bam.sort.fastq.unmapped.sam.sort.bam", "56752_WT_Naturally_1.bam.sort.fastq.unmapped.sam.sort.bam", "56751_tt_6_days_3.bam.sort.fastq.unmapped.sam.sort.bam", "56750_tt_6_days_2.bam.sort.fastq.unmapped.sam.sort.bam", "56749_tt_6_days_1.bam.sort.fastq.unmapped.sam.sort.bam", "56748_tt_0_days_3.bam.sort.fastq.unmapped.sam.sort.bam", "56747_tt_0_days_2.bam.sort.fastq.unmapped.sam.sort.bam", "56746_tt_0_days_1.bam.sort.fastq.unmapped.sam.sort.bam", "56745_WT_10_days_3.bam.sort.fastq.unmapped.sam.sort.bam", "56744_WT_10_days_2.bam.sort.fastq.unmapped.sam.sort.bam", "56743_WT_10_days_1.bam.sort.fastq.unmapped.sam.sort.bam", "56742_WT_6_days_3.bam.sort.fastq.unmapped.sam.sort.bam", "56741_WT_6_days_2.bam.sort.fastq.unmapped.sam.sort.bam", "56740_WT_6_days_1.bam.sort.fastq.unmapped.sam.sort.bam", "56739_WT_0_days_3.bam.sort.fastq.unmapped.sam.sort.bam", "56738_WT_0_days_2.bam.sort.fastq.unmapped.sam.sort.bam", "56737_WT_0_days_1.bam.sort.fastq.unmapped.sam.sort.bam", "56736_tt_T1_tt_6d_3.bam.sort.fastq.unmapped.sam.sort.bam", "56735_tt_T1_tt_6d_2.bam.sort.fastq.unmapped.sam.sort.bam", "56734_tt_T1_tt_6d_1.bam.sort.fastq.unmapped.sam.sort.bam", "56733_tt_T1_tt_0d_3.bam.sort.fastq.unmapped.sam.sort.bam", "56732_tt_T1_tt_0d_2.bam.sort.fastq.unmapped.sam.sort.bam", "56731_tt_T1_tt_0d_1.bam.sort.fastq.unmapped.sam.sort.bam", "56730_tt_T1_tt_0d_3.bam.sort.fastq.unmapped.sam.sort.bam", "56729_tt_T1_tt_0d_2.bam.sort.fastq.unmapped.sam.sort.bam", "56728_tt_T1_tt_0d_1.bam.sort.fastq.unmapped.sam.sort.bam", "56727_WT_T1_NA_3.bam.sort.fastq.unmapped.sam.sort.bam", "56726_WT_T1_NA_2.bam.sort.fastq.unmapped.sam.sort.bam", "56725_WT_T1_NA_1.bam.sort.fastq.unmapped.sam.sort.bam", "56724_WT_T1_WT_0d_3.bam.sort.fastq.unmapped.sam.sort.bam", "56723_WT_T1_WT_0d_2.bam.sort.fastq.unmapped.sam.sort.bam", "56722_WT_T1_WT_0d_1.bam.sort.fastq.unmapped.sam.sort.bam", "56721_WT_T1_WT_10d_3.bam.sort.fastq.unmapped.sam.sort.bam", "56720_WT_T1_WT_10d_2.bam.sort.fastq.unmapped.sam.sort.bam", "56719_WT_T1_WT_10d_1.bam.sort.fastq.unmapped.sam.sort.bam", "56718_WT_T1_WT_0d_3.bam.sort.fastq.unmapped.sam.sort.bam", "56717_WT_T1_WT_0d_2.bam.sort.fastq.unmapped.sam.sort.bam", "56716_WT_T1_WT_0d_1.bam.sort.fastq.unmapped.sam.sort.bam", "56715_WT_T1_WT_6d_3.bam.sort.fastq.unmapped.sam.sort.bam", "56714_WT_T1_WT_6d_2.bam.sort.fastq.unmapped.sam.sort.bam", "56713_WT_T1_WT_6d_1.bam.sort.fastq.unmapped.sam.sort.bam", "56712_WT_T1_WT_0d_3.bam.sort.fastq.unmapped.sam.sort.bam", "56711_WT_T1_WT_0d_2.bam.sort.fastq.unmapped.sam.sort.bam", "56710_WT_T1_WT_0d_1.bam.sort.fastq.unmapped.sam.sort.bam", "56709_WT_T1_WT_0d_3.bam.sort.fastq.unmapped.sam.sort.bam", "56708_WT_T1_WT_0d_2.bam.sort.fastq.unmapped.sam.sort.bam", "56707_WT_T1_WT_0d_1.bam.sort.fastq.unmapped.sam.sort.bam", "56706_WT_T1_tt_0d_3.bam.sort.fastq.unmapped.sam.sort.bam", "56705_WT_T1_tt_0d_2.bam.sort.fastq.unmapped.sam.sort.bam", "56704_WT_T1_tt_0d_1.bam.sort.fastq.unmapped.sam.sort.bam")</span>
+ <span class="co1"># #librariesName <- c("80484_Celery_3_day_imbibed_embryo_20C_rep_3_3.bam.sort.fastq.unmapped.concordant_uniqsort.bam_reads.Celery_genome_GG_trinity.500bp_new.sam.sort.bam", "80483_Celery_3_day_imbibed_embryo_20C_rep_2_2.bam.sort.fastq.unmapped.concordant_uniqsort.bam_reads.Celery_genome_GG_trinity.500bp_new.sam.sort.bam", "80482_Celery_3_day_imbibed_embryo_20C_rep_1_1.bam.sort.fastq.unmapped.concordant_uniqsort.bam_reads.Celery_genome_GG_trinity.500bp_new.sam.sort.bam", "80481_Celery_1_day_imbibed_embryo_20C_rep_3_3.bam.sort.fastq.unmapped.concordant_uniqsort.bam_reads.Celery_genome_GG_trinity.500bp_new.sam.sort.bam", "80480_Celery_1_day_imbibed_embryo_20C_rep_2_2.bam.sort.fastq.unmapped.concordant_uniqsort.bam_reads.Celery_genome_GG_trinity.500bp_new.sam.sort.bam", "80479_Celery_1_day_imbibed_embryo_20C_rep_1_1.bam.sort.fastq.unmapped.concordant_uniqsort.bam_reads.Celery_genome_GG_trinity.500bp_new.sam.sort.bam", "80478_Celery_5_day_imbibed_whole_fruit_29C_rep_3_3.bam.sort.fastq.unmapped.concordant_uniqsort.bam_reads.Celery_genome_GG_trinity.500bp_new.sam.sort.bam", "80477_Celery_5_day_imbibed_whole_fruit_29C_rep_2_2.bam.sort.fastq.unmapped.concordant_uniqsort.bam_reads.Celery_genome_GG_trinity.500bp_new.sam.sort.bam", "80460_Celery_3_day_imbibed_whole_fruit_20C_rep_2_2.bam.sort.fastq.unmapped.concordant_uniqsort.bam_reads.Celery_genome_GG_trinity.500bp_new.sam.sort.bam", "80459_Celery_3_day_imbibed_whole_fruit_20C_rep_1_1.bam.sort.fastq.unmapped.concordant_uniqsort.bam_reads.Celery_genome_GG_trinity.500bp_new.sam.sort.bam", "80458_Celery_1_day_imbibed_whole_fruit_20C_rep_3_3.bam.sort.fastq.unmapped.concordant_uniqsort.bam_reads.Celery_genome_GG_trinity.500bp_new.sam.sort.bam", "80457_Celery_1_day_imbibed_whole_fruit_20C_rep_2_2.bam.sort.fastq.unmapped.concordant_uniqsort.bam_reads.Celery_genome_GG_trinity.500bp_new.sam.sort.bam", "80456_Celery_1_day_imbibed_whole_fruit_20C_rep_1_1.bam.sort.fastq.unmapped.concordant_uniqsort.bam_reads.Celery_genome_GG_trinity.500bp_new.sam.sort.bam", "80455_Celery_Dry_whole_fruit_rep_3_3.bam.sort.fastq.unmapped.concordant_uniqsort.bam_reads.Celery_genome_GG_trinity.500bp_new.sam.sort.bam", "80454_Celery_Dry_whole_fruit_rep_2_2.bam.sort.fastq.unmapped.concordant_uniqsort.bam_reads.Celery_genome_GG_trinity.500bp_new.sam.sort.bam", "80453_Celery_Dry_whole_fruit_rep_1_1.bam.sort.fastq.unmapped.concordant_uniqsort.bam_reads.Celery_genome_GG_trinity.500bp_new.sam.sort.bam", "80452_Celery_5_day_imbibed_whole_fruit_29C_rep_1_1.bam.sort.fastq.unmapped.concordant_uniqsort.bam_reads.Celery_genome_GG_trinity.500bp_new.sam.sort.bam", "80451_Celery_5_day_imbibed_whole_fruit_100uM_ABA_20C_rep_3_3.bam.sort.fastq.unmapped.concordant_uniqsort.bam_reads.Celery_genome_GG_trinity.500bp_new.sam.sort.bam", "80450_Celery_5_day_imbibed_whole_fruit_100uM_ABA_20C_rep_2_2.bam.sort.fastq.unmapped.concordant_uniqsort.bam_reads.Celery_genome_GG_trinity.500bp_new.sam.sort.bam", "80449_Celery_5_day_imbibed_whole_fruit_100uM_ABA_20C_rep_1_1.bam.sort.fastq.unmapped.concordant_uniqsort.bam_reads.Celery_genome_GG_trinity.500bp_new.sam.sort.bam", "80448_Celery_5_day_imbibed_whole_fruit_20C_rep_3_3.bam.sort.fastq.unmapped.concordant_uniqsort.bam_reads.Celery_genome_GG_trinity.500bp_new.sam.sort.bam", "80447_Celery_5_day_imbibed_whole_fruit_20C_rep_2_2.bam.sort.fastq.unmapped.concordant_uniqsort.bam_reads.Celery_genome_GG_trinity.500bp_new.sam.sort.bam", "80446_Celery_5_day_imbibed_whole_fruit_20C_rep_1_1.bam.sort.fastq.unmapped.concordant_uniqsort.bam_reads.Celery_genome_GG_trinity.500bp_new.sam.sort.bam", "80445_Celery_3_day_imbibed_whole_fruit_20C_rep_3_3.bam.sort.fastq.unmapped.concordant_uniqsort.bam_reads.Celery_genome_GG_trinity.500bp_new.sam.sort.bam.featureCounts.p.txt")</span>
+ <span class="co1"># romanNumber <- c("T17_Dry_Naturally_Freezedryseed", "T17_Dry_Naturally_Freezedryseed.1", "T17_Dry_Naturally_Freezedryseed.2", "T16_Dry_6days_Freezeafter6dageing", "T16_Dry_6days_Freezeafter6dageing.1", "T16_Dry_6days_Freezeafter6dageing.2", "T15_Dry_0days_Freezedryseed", "T15_Dry_0days_Freezedryseed.1", "T15_Dry_0days_Freezedryseed.2", "T14_Dry_10days_Freezeafter10dageing", "T14_Dry_10days_Freezeafter10dageing.1", "T14_Dry_10days_Freezeafter10dageing.2", "T13_Dry_6days_Freezeafter6dageing", "T13_Dry_6days_Freezeafter6dageing.1", "T13_Dry_6days_Freezeafter6dageing.2", "T12_Dry_0days_Freezedryseed", "T12_Dry_0days_Freezedryseed.1", "T12_Dry_0days_Freezedryseed.2", "T11_Imbibe_6days_12h", "T11_Imbibe_6days_12h.1", "T11_Imbibe_6days_12h.2", "T10_Imbibe_6days_5h", "T10_Imbibe_6days_5h.1", "T10_Imbibe_6days_5h.2", "T9_Imbibe_0dyas_5h", "T9_Imbibe_0dyas_5h.1", "T9_Imbibe_0dyas_5h.2", "T8_Imbibe_Naturally_47h", "T8_Imbibe_Naturally_47h.1", "T8_Imbibe_Naturally_47h.2", "T7_Imbibe_Naturally_24h", "T7_Imbibe_Naturally_24h.1", "T7_Imbibe_Naturally_24h.2", "T6_Imbibe_10days_72h", "T6_Imbibe_10days_72h.1", "T6_Imbibe_10days_72h.2", "T5_Imbibe_10days_24h", "T5_Imbibe_10days_24h.1", "T5_Imbibe_10days_24h.2", "T4_Imbibe_6days_47h", "T4_Imbibe_6days_47h.1", "T4_Imbibe_6days_47h.2", "T3_Imbibe_6days_24h", "T3_Imbibe_6days_24h.1", "T3_Imbibe_6days_24h.2", "T2_Imbibe_0days_24h", "T2_Imbibe_0days_24h.1", "T2_Imbibe_0days_24h.2", "T1_Imbibe_0days_5h", "T1_Imbibe_0days_5h.1", "T1_Imbibe_0days_5h.2")</span>
+ <span class="co1"># #romanNumber <- c("emb_3d_20.2", "emb_3d_20.1", "emb_3d_20", "emb_1d_20.2", "emb_1d_20.1", "emb_1d_20", "wf_5d_29.2", "wf_5d_29.1", "wf_3d_20.1", "wf_3d_20", "wf_1d_20.2", "wf_1d_20.1", "wf_1d_20", "wf_dry.2", "wf_dry.1", "wf_dry", "wf_5d_29", "wf_5d_ABA_20.2", "wf_5d_ABA_20.1", "wf_5d_ABA_20", "wf_5d_20.2", "wf_5d_20.1", "wf_5d_20", "wf_3d_20.2")</span>
+ <span class="co1"># </span>
+ <span class="co1"># </span>
+ <span class="co1"># for(i in 1:length(librariesName)) {</span>
+ <span class="co1"># colnames(data0)[colnames(data0)==grep(librariesName[i], names(data0), value = TRUE)] <- romanNumber[i]</span>
+ <span class="co1"># }</span>
+
+ <span class="co1"># creats a list of the column names/samples you would like to compare</span>
+ SampleNames <span class="sy0"><-</span> makeSampleList<span class="br0">(</span>sampleNameI, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/length.html"><span class="kw2">length</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/grep.html"><span class="kw2">grep</span></a><span class="br0">(</span>paste0<span class="br0">(</span><span class="st0">"^"</span>,sampleNameI,<span class="st0">"[^A-Z]"</span><span class="br0">)</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/colnames.html"><span class="kw2">colnames</span></a><span class="br0">(</span>data0<span class="br0">)</span><span class="br0">)</span><span class="br0">)</span> <span class="sy0">+</span> <span class="nu0">1</span>,
+ sampleNameII, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/length.html"><span class="kw2">length</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/grep.html"><span class="kw2">grep</span></a><span class="br0">(</span>paste0<span class="br0">(</span><span class="st0">"^"</span>,sampleNameII,<span class="st0">"[^A-Z]"</span><span class="br0">)</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/colnames.html"><span class="kw2">colnames</span></a><span class="br0">(</span>data0<span class="br0">)</span><span class="br0">)</span><span class="br0">)</span> <span class="sy0">+</span> <span class="nu0">1</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span>SampleNames<span class="br0">)</span>
+
+ <span class="co1">## mal anschauen als ersatz für das darüber ##</span>
+ <span class="co1">## newenw <- table.new[, grepl(paste(LIST,collapse="|"), colnames(table.new))]</span>
+
+
+ <span class="co1"># exctract the samples from the data0 if needed</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/if.html"><span class="kw2">if</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/length.html"><span class="kw2">length</span></a><span class="br0">(</span>SampleNames<span class="br0">)</span> <span class="sy0">></span> <span class="nu0">0</span><span class="br0">)</span> <span class="br0">{</span>
+ RTableInFiles <span class="sy0"><-</span> data0<span class="br0">[</span>,SampleNames<span class="br0">]</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/data.html"><span class="kw8">data</span></a> <span class="sy0"><-</span> data0<span class="br0">[</span>,SampleNames<span class="br0">]</span>
+ <span class="br0">}</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/head.html"><span class="kw8">head</span></a><span class="br0">(</span>RTableInFiles<span class="br0">)</span><span class="br0">)</span>
+
+ <span class="co1"># sort by column name</span>
+ <span class="co1"># data <- data[ , order(names(data))] # dangeros, the order of query and referenz might be not the same</span>
+ <span class="co1"># see how many rows and columns are in the tables</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/paste.html"><span class="kw2">paste</span></a><span class="br0">(</span><span class="st0">"Raw data row number: "</span>,<a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/nrow.html"><span class="kw2">nrow</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/data.html"><span class="kw8">data</span></a><span class="br0">)</span><span class="br0">)</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/paste.html"><span class="kw2">paste</span></a><span class="br0">(</span><span class="st0">"Raw data column number: "</span>,<a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/ncol.html"><span class="kw2">ncol</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/data.html"><span class="kw8">data</span></a><span class="br0">)</span><span class="br0">)</span><span class="br0">)</span>
+
+ <span class="co1"># 2) A typical differential expression analysis workflow</span>
+ <span class="co1"># 2.1) Filtering and exploratory data analysis</span>
+ <span class="co1"># filter: One single gene/spike-in must have at least 5 counts in minimum 2 libraries</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/stats/html/filter.html"><span class="kw7">filter</span></a> <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/apply.html"><span class="kw2">apply</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/data.html"><span class="kw8">data</span></a>, <span class="nu0">1</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/function.html"><span class="kw2">function</span></a><span class="br0">(</span>x<span class="br0">)</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/length.html"><span class="kw2">length</span></a><span class="br0">(</span>x<span class="br0">[</span>x<span class="sy0">></span><span class="nu0">5</span><span class="br0">]</span><span class="br0">)</span><span class="sy0">>=</span><span class="nu0">2</span><span class="br0">)</span>
+ dataFiltered <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/data.html"><span class="kw8">data</span></a><span class="br0">[</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/stats/html/filter.html"><span class="kw7">filter</span></a>,<span class="br0">]</span>
+ <span class="co1"># see how many rows and columns are left</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/paste.html"><span class="kw2">paste</span></a><span class="br0">(</span><span class="st0">"Filtered data row number: "</span>,<a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/nrow.html"><span class="kw2">nrow</span></a><span class="br0">(</span>dataFiltered<span class="br0">)</span><span class="br0">)</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/paste.html"><span class="kw2">paste</span></a><span class="br0">(</span><span class="st0">"Filtered data row number: "</span>,<a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/ncol.html"><span class="kw2">ncol</span></a><span class="br0">(</span>dataFiltered<span class="br0">)</span><span class="br0">)</span><span class="br0">)</span>
+ <span class="co1"># filter gene names</span>
+ genes <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/rownames.html"><span class="kw2">rownames</span></a><span class="br0">(</span>dataFiltered<span class="br0">)</span><span class="br0">[</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/grep.html"><span class="kw2">grep</span></a><span class="br0">(</span><span class="st0">"^Pp3"</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/rownames.html"><span class="kw2">rownames</span></a><span class="br0">(</span>dataFiltered<span class="br0">)</span><span class="br0">)</span><span class="br0">]</span>
+ <span class="co1"># filter spike-in names</span>
+ spikes <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/rownames.html"><span class="kw2">rownames</span></a><span class="br0">(</span>dataFiltered<span class="br0">)</span><span class="br0">[</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/grep.html"><span class="kw2">grep</span></a><span class="br0">(</span><span class="st0">"^ERCC"</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/rownames.html"><span class="kw2">rownames</span></a><span class="br0">(</span>dataFiltered<span class="br0">)</span><span class="br0">)</span><span class="br0">]</span>
+ <span class="co1"># get the column name list as.factors</span>
+ xtmp <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/colnames.html"><span class="kw2">colnames</span></a><span class="br0">(</span>dataFiltered<span class="br0">)</span>
+ x <span class="sy0"><-</span> split2list<span class="br0">(</span>xtmp<span class="br0">)</span>
+
+ sampleNameList <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/gsub.html"><span class="kw2">gsub</span></a><span class="br0">(</span><span class="st0">".[1234567890]+$"</span>, <span class="st0">""</span>, SampleNames<span class="br0">)</span>
+ columnPos <span class="sy0"><-</span> makeIndexList<span class="br0">(</span>SampleNames<span class="br0">)</span>
+
+ <span class="co1"># run ...</span>
+ <span class="co1">### edgeR ###</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span>paste0<span class="br0">(</span><span class="st0">"edgeR is running with "</span>, cName<span class="br0">)</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/packageDescription.html"><span class="kw8">packageDescription</span></a><span class="br0">(</span><span class="st0">"edgeR"</span><span class="br0">)</span>
+ edgeRFunction<span class="br0">(</span>outdir, edgeRDir, cName, RTableInFiles, pvtedgeR, sampleNameI, sampleNameII, sampleNameList<span class="br0">)</span>
+
+ <span class="co1">#### DESeq2 ####</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span>paste0<span class="br0">(</span><span class="st0">"DESeq2 is running with "</span>, cName<span class="br0">)</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/packageDescription.html"><span class="kw8">packageDescription</span></a><span class="br0">(</span><span class="st0">"DESeq2"</span><span class="br0">)</span>
+ DESeq2Function<span class="br0">(</span>outdir, DESeq2Dir, cName, RTableInFiles, pvtDESeq2, sampleNameI, sampleNameII, sampleNameList<span class="br0">)</span>
+
+ <span class="co1">### NOISeq ###</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span>paste0<span class="br0">(</span><span class="st0">"NOISeq is running with "</span>, cName<span class="br0">)</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/packageDescription.html"><span class="kw8">packageDescription</span></a><span class="br0">(</span><span class="st0">"NOISeq"</span><span class="br0">)</span>
+ NOISeqFunction<span class="br0">(</span>outdir, NOISeqDir, cName, RTableInFiles, pvtNOISeq, sampleNameI, sampleNameII, myLenPos, myGCPos, LenGCTable, columnPos, sampleNameList, SampleNames<span class="br0">)</span>
+
+ <span class="co1">### Overlap of all three methods ###</span>
+ <span class="co1"># intersection with DEG direction check => 1, without => 0</span>
+ intersection_4.<span class="me1">file</span> <span class="sy0"><-</span> intersection<span class="br0">(</span>outdir,<span class="nu0">1</span>,<span class="nu0">4</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/write.table.html"><span class="kw8">write.<span class="me1">table</span></span></a><span class="br0">(</span>intersection_4.<span class="me1">file</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/file.html"><span class="kw2">file</span></a> <span class="sy0">=</span> paste0<span class="br0">(</span>outdir, <span class="st0">"/"</span>, cName,<span class="st0">"_intersection_four_methods_"</span>,<a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/nrow.html"><span class="kw2">nrow</span></a><span class="br0">(</span>intersection_4.<span class="me1">file</span><span class="br0">)</span>,<span class="st0">".tsv"</span><span class="br0">)</span>, sep <span class="sy0">=</span> <span class="st0">"<span class="es0">\t</span>"</span>, col.<span class="me1">names</span> <span class="sy0">=</span> TRUE, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/row.names.html"><span class="kw2">row.<span class="me1">names</span></span></a> <span class="sy0">=</span> TRUE, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/quote.html"><span class="kw2">quote</span></a> <span class="sy0">=</span> FALSE<span class="br0">)</span>
+ <span class="co1"># edgeR, DESeq2, NOISeq</span>
+ intersection_3.<span class="me1">file</span> <span class="sy0"><-</span> intersection<span class="br0">(</span>outdir,<span class="nu0">1</span>,<span class="nu0">3</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/write.table.html"><span class="kw8">write.<span class="me1">table</span></span></a><span class="br0">(</span>intersection_3.<span class="me1">file</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/file.html"><span class="kw2">file</span></a> <span class="sy0">=</span> paste0<span class="br0">(</span>outdir, <span class="st0">"/"</span>, cName,<span class="st0">"_intersection_three_methods_"</span>,<a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/nrow.html"><span class="kw2">nrow</span></a><span class="br0">(</span>intersection_3.<span class="me1">file</span><span class="br0">)</span>,<span class="st0">".tsv"</span><span class="br0">)</span>, sep <span class="sy0">=</span> <span class="st0">"<span class="es0">\t</span>"</span>, col.<span class="me1">names</span> <span class="sy0">=</span> TRUE, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/row.names.html"><span class="kw2">row.<span class="me1">names</span></span></a> <span class="sy0">=</span> TRUE, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/quote.html"><span class="kw2">quote</span></a> <span class="sy0">=</span> FALSE<span class="br0">)</span>
+
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/sink.html"><span class="kw2">sink</span></a><span class="br0">(</span><span class="br0">)</span> <span class="co1"># End of log file</span>
+
+<span class="br0">}</span>
+
+
+
+
+
+<span class="co1">####################</span>
+<span class="co1">## main functions #</span>
+<span class="co1">####################</span>
+
+plotGraphics <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/function.html"><span class="kw2">function</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/data.html"><span class="kw8">data</span></a>, librariesName, cName, outdir, romanNumber<span class="br0">)</span>
+<span class="br0">{</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/library.html"><span class="kw2">library</span></a><span class="br0">(</span><span class="st0">"DESeq2"</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/library.html"><span class="kw2">library</span></a><span class="br0">(</span><span class="st0">"ggplot2"</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/library.html"><span class="kw2">library</span></a><span class="br0">(</span><span class="st0">"RColorBrewer"</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/library.html"><span class="kw2">library</span></a><span class="br0">(</span><span class="st0">"pheatmap"</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/library.html"><span class="kw2">library</span></a><span class="br0">(</span><span class="st0">"genefilter"</span><span class="br0">)</span>
+
+ <span class="co1"># create sample annotation lists</span>
+ <span class="co1"># sample.name.list <- gsub(".[12]", "", librariesName[colnames(data)])</span>
+ sample.<span class="me1">name</span>.<span class="me1">list</span> <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/gsub.html"><span class="kw2">gsub</span></a><span class="br0">(</span><span class="st0">".[12]"</span>, <span class="st0">""</span>, romanNumber<span class="br0">)</span>
+ sample.<span class="me1">name</span>.<span class="me1">uniq</span> <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/unique.html"><span class="kw2">unique</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/unlist.html"><span class="kw2">unlist</span></a><span class="br0">(</span>sample.<span class="me1">name</span>.<span class="me1">list</span>, use.<span class="me1">names</span> <span class="sy0">=</span> FALSE<span class="br0">)</span><span class="br0">)</span>
+
+ col.<span class="me1">data</span>.<span class="me1">condition</span> <span class="sy0">=</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/data.frame.html"><span class="kw2">data.<span class="me1">frame</span></span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/row.names.html"><span class="kw2">row.<span class="me1">names</span></span></a> <span class="sy0">=</span> librariesName, condition <span class="sy0">=</span> sample.<span class="me1">name</span>.<span class="me1">list</span><span class="br0">)</span>
+
+ <span class="co1"># run DESeq2 functions</span>
+ dds.<span class="me1">matrix</span> <span class="sy0"><-</span> DESeqDataSetFromMatrix<span class="br0">(</span>countData <span class="sy0">=</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/data.html"><span class="kw8">data</span></a>, colData <span class="sy0">=</span> col.<span class="me1">data</span>.<span class="me1">condition</span>, design <span class="sy0">=</span> ~condition<span class="br0">)</span> <span class="co1"># data must be integer! (Ganze Zahlen)</span>
+ colData<span class="br0">(</span>dds.<span class="me1">matrix</span><span class="br0">)</span>$condition <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/factor.html"><span class="kw2">factor</span></a><span class="br0">(</span>colData<span class="br0">(</span>dds.<span class="me1">matrix</span><span class="br0">)</span>$condition, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/levels.html"><span class="kw2">levels</span></a> <span class="sy0">=</span> sample.<span class="me1">name</span>.<span class="me1">uniq</span><span class="br0">)</span>
+ dds.<span class="me1">matrix</span>.<span class="me1">deseq</span> <span class="sy0"><-</span> DESeq<span class="br0">(</span>dds.<span class="me1">matrix</span><span class="br0">)</span>
+ dds.<span class="me1">matrix</span>.<span class="me1">res</span> <span class="sy0"><-</span> results<span class="br0">(</span>dds.<span class="me1">matrix</span>.<span class="me1">deseq</span><span class="br0">)</span>
+ dds.<span class="me1">matrix</span>.<span class="me1">res</span> <span class="sy0"><-</span> dds.<span class="me1">matrix</span>.<span class="me1">res</span><span class="br0">[</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/order.html"><span class="kw2">order</span></a><span class="br0">(</span>dds.<span class="me1">matrix</span>.<span class="me1">res</span>$padj<span class="br0">)</span>, <span class="br0">]</span>
+ dds.<span class="me1">matrix</span>.<span class="me1">res</span>.<span class="me1">fdr</span> <span class="sy0"><-</span> dds.<span class="me1">matrix</span>.<span class="me1">res</span><span class="br0">[</span><span class="sy0">!</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/is.na.html"><span class="kw2">is.<span class="me1">na</span></span></a><span class="br0">(</span>dds.<span class="me1">matrix</span>.<span class="me1">res</span>$padj<span class="br0">)</span>, <span class="br0">]</span>
+ dds.<span class="me1">matrix</span>.<span class="me1">res</span>.<span class="me1">fdr</span> <span class="sy0"><-</span> dds.<span class="me1">matrix</span>.<span class="me1">res</span>.<span class="me1">fdr</span><span class="br0">[</span>dds.<span class="me1">matrix</span>.<span class="me1">res</span>.<span class="me1">fdr</span>$padj <span class="sy0"><</span> <span class="nu0">0.0001</span>, <span class="br0">]</span>
+ dds.<span class="me1">matrix</span>.<span class="me1">rld</span> <span class="sy0"><-</span> rlogTransformation<span class="br0">(</span>dds.<span class="me1">matrix</span>, blind <span class="sy0">=</span> TRUE<span class="br0">)</span>
+
+ <span class="co1"># data for PCA plot</span>
+ pcaData <span class="sy0"><-</span> plotPCA<span class="br0">(</span>dds.<span class="me1">matrix</span>.<span class="me1">rld</span>, intgroup <span class="sy0">=</span> <span class="st0">"condition"</span>, returnData<span class="sy0">=</span>TRUE<span class="br0">)</span>
+ percentVar <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/round.html"><span class="kw2">round</span></a><span class="br0">(</span><span class="nu0">100</span> <span class="sy0">*</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/attr.html"><span class="kw2">attr</span></a><span class="br0">(</span>pcaData, <span class="st0">"percentVar"</span><span class="br0">)</span><span class="br0">)</span>
+ <span class="co1"># color for samples</span>
+ sample.<span class="me1">colors</span> <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span><span class="st0">"gray60"</span>,<span class="st0">"#D73027"</span>,<span class="st0">"#4575B4"</span>, <span class="st0">"purple"</span>, <span class="st0">"orange"</span>,<span class="st0">"#113FF7"</span>,<span class="st0">"green"</span>, <span class="st0">"black"</span><span class="br0">)</span>
+
+ <span class="co1"># plot the PCA</span>
+ <span class="co1"># https://cran.r-project.org/web/packages/ggfortify/vignettes/plot_pca.html</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/png.html"><span class="kw5">png</span></a><span class="br0">(</span>filename<span class="sy0">=</span>paste0<span class="br0">(</span>outdir,<span class="st0">"PCA_all_samples_DEseq2_normalized.png"</span><span class="br0">)</span><span class="br0">)</span>
+ ggplot<span class="br0">(</span>
+ pcaData,
+ aes<span class="br0">(</span>
+ PC1,
+ PC2,
+ color<span class="sy0">=</span>condition,
+ shape<span class="sy0">=</span>condition<span class="br0">)</span>
+ <span class="br0">)</span> <span class="sy0">+</span>
+ scale_shape_manual<span class="br0">(</span>values <span class="sy0">=</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span><span class="nu0">4</span>, <span class="nu0">1</span>, <span class="nu0">2</span>, <span class="nu0">3</span>, <span class="nu0">0</span>, <span class="nu0">5</span>, <span class="nu0">6</span>, <span class="nu0">7</span><span class="br0">)</span><span class="br0">)</span> <span class="sy0">+</span>
+ geom_point<span class="br0">(</span>size<span class="sy0">=</span><span class="nu0">2.5</span><span class="br0">)</span> <span class="sy0">+</span>
+ xlab<span class="br0">(</span>
+ paste0<span class="br0">(</span><span class="st0">"PC1: "</span>,percentVar<span class="br0">[</span><span class="nu0">1</span><span class="br0">]</span>,<span class="st0">"% variance"</span><span class="br0">)</span>
+ <span class="br0">)</span> <span class="sy0">+</span>
+ ylab<span class="br0">(</span>
+ paste0<span class="br0">(</span><span class="st0">"PC2: "</span>,percentVar<span class="br0">[</span><span class="nu0">2</span><span class="br0">]</span>,<span class="st0">"% variance"</span><span class="br0">)</span>
+ <span class="br0">)</span> <span class="sy0">+</span>
+ theme<span class="br0">(</span><span class="br0">)</span> <span class="sy0">+</span> <span class="co1">#, face="bold"</span>
+ scale_colour_manual<span class="br0">(</span>
+ values<span class="sy0">=</span>sample.<span class="me1">colors</span> <span class="co1"># dodgerblue3</span>
+ <span class="br0">)</span> <span class="sy0">+</span>
+ ggtitle<span class="br0">(</span><span class="st0">"PCA of all samples (DESeq2 normalized)"</span><span class="br0">)</span> <span class="sy0">+</span>
+ theme<span class="br0">(</span>
+ plot.<span class="me1">title</span> <span class="sy0">=</span> element_text<span class="br0">(</span>lineheight<span class="sy0">=</span>.8<span class="br0">)</span>,
+ panel.<span class="me1">background</span> <span class="sy0">=</span> element_rect<span class="br0">(</span>fill <span class="sy0">=</span> <span class="st0">"gray95"</span><span class="br0">)</span>
+ <span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/dev.off.html"><span class="kw5">dev.<span class="me1">off</span></span></a><span class="br0">(</span><span class="br0">)</span>
+
+ <span class="co1"># how many genes will be involved in the heatmap calculation</span>
+ numbGenes <span class="sy0"><-</span> <span class="nu0">100</span>
+ <span class="co1"># pheatmap data</span>
+ topVarGenes <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/head.html"><span class="kw8">head</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/order.html"><span class="kw2">order</span></a><span class="br0">(</span>rowVars<span class="br0">(</span>assay<span class="br0">(</span>dds.<span class="me1">matrix</span>.<span class="me1">rld</span><span class="br0">)</span><span class="br0">)</span>,decreasing<span class="sy0">=</span>TRUE<span class="br0">)</span>,numbGenes<span class="br0">)</span>
+ mat <span class="sy0"><-</span> assay<span class="br0">(</span>dds.<span class="me1">matrix</span>.<span class="me1">rld</span><span class="br0">)</span><span class="br0">[</span> topVarGenes, <span class="br0">]</span>
+ mat <span class="sy0"><-</span> mat <span class="sy0">-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/rowMeans.html"><span class="kw2">rowMeans</span></a><span class="br0">(</span>mat<span class="br0">)</span>
+ <span class="co1"># pheatmap data annotation</span>
+ anno <span class="sy0"><-</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/as.data.frame.html"><span class="kw2">as.<span class="me1">data</span>.<span class="me1">frame</span></span></a><span class="br0">(</span>colData<span class="br0">(</span>dds.<span class="me1">matrix</span>.<span class="me1">rld</span><span class="br0">)</span><span class="br0">[</span>,<a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span><span class="st0">"condition"</span><span class="br0">)</span><span class="br0">]</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/rownames.html"><span class="kw2">rownames</span></a><span class="br0">(</span>anno<span class="br0">)</span> <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/colnames.html"><span class="kw2">colnames</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/data.html"><span class="kw8">data</span></a><span class="br0">)</span> <span class="co1"># check out the row names of annotation</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/colnames.html"><span class="kw2">colnames</span></a><span class="br0">(</span>anno<span class="br0">)</span> <span class="sy0"><-</span> <span class="st0">"condition"</span>
+ <span class="co1"># pheatmap data annotation color</span>
+ condition <span class="sy0"><-</span> sample.<span class="me1">colors</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/names.html"><span class="kw2">names</span></a><span class="br0">(</span>condition<span class="br0">)</span> <span class="sy0"><-</span> sample.<span class="me1">name</span>.<span class="me1">uniq</span>
+ anno_colors <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/list.html"><span class="kw2">list</span></a><span class="br0">(</span>condition <span class="sy0">=</span> condition<span class="br0">)</span>
+
+ <span class="co1">#heatmap(mat)</span>
+ <span class="co1">#pheatmap(mat)</span>
+ <span class="co1"># ftp://cran.r-project.org/pub/R/web/packages/pheatmap/pheatmap.pdf</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/png.html"><span class="kw5">png</span></a><span class="br0">(</span>filename<span class="sy0">=</span>paste0<span class="br0">(</span>outdir,<span class="st0">"HC_heatmap_all_samples_DESeq2_normalized.png"</span><span class="br0">)</span><span class="br0">)</span>
+ pheatmap<span class="br0">(</span>mat ,
+ annotation <span class="sy0">=</span> anno,
+ annotation_colors <span class="sy0">=</span> anno_colors,
+ fontsize <span class="sy0">=</span> <span class="nu0">10</span>,
+ fontsize_row <span class="sy0">=</span> <span class="nu0">6</span>,
+ fontsize_col <span class="sy0">=</span> <span class="nu0">10</span>,
+ main <span class="sy0">=</span> paste0<span class="br0">(</span><span class="st0">"Heatmap of all samples (DESeq2 normalized) "</span>, numbGenes,<span class="st0">" genes<span class="es0">\n</span>"</span><span class="br0">)</span>,
+ annotation_names_col <span class="sy0">=</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/F.html"><span class="kw2">F</span></a>,
+ show_rownames <span class="sy0">=</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/F.html"><span class="kw2">F</span></a>,
+ cluster_rows <span class="sy0">=</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/F.html"><span class="kw2">F</span></a>,
+ border_color <span class="sy0">=</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/F.html"><span class="kw2">F</span></a>,
+ treeheight_col <span class="sy0">=</span> <span class="nu0">20</span>
+ <span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/dev.off.html"><span class="kw5">dev.<span class="me1">off</span></span></a><span class="br0">(</span><span class="br0">)</span>
+<span class="br0">}</span>
+
+
+edgeRFunction <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/function.html"><span class="kw2">function</span></a><span class="br0">(</span>odir, edgeRDir, cName, RTableInFiles, pvtedgeR, sampleNameI, sampleNameII, sampleNameList<span class="br0">)</span>
+<span class="br0">{</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/library.html"><span class="kw2">library</span></a><span class="br0">(</span>edgeR<span class="br0">)</span>
+
+ outdir <span class="sy0"><-</span> paste0<span class="br0">(</span>odir, <span class="st0">"/"</span>,edgeRDir,<span class="st0">"/"</span><span class="br0">)</span> <span class="co1"># set outdir</span>
+
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/dir.create.html"><span class="kw2">dir.<span class="me1">create</span></span></a><span class="br0">(</span>outdir, showWarnings <span class="sy0">=</span> FALSE<span class="br0">)</span> <span class="co1"># create output folder</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/dir.create.html"><span class="kw2">dir.<span class="me1">create</span></span></a><span class="br0">(</span>paste0<span class="br0">(</span>outdir,<span class="st0">"plots"</span><span class="br0">)</span>, showWarnings <span class="sy0">=</span> FALSE<span class="br0">)</span> <span class="co1"># create subfolder "plots"</span>
+
+ comparison <span class="sy0"><-</span> cName
+ counts <span class="sy0"><-</span> RTableInFiles
+
+ pvt <span class="sy0"><-</span> pvtedgeR
+
+ group <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/factor.html"><span class="kw2">factor</span></a><span class="br0">(</span>sampleNameList<span class="br0">)</span>
+
+ <span class="co1"># edgeR 'normal'</span>
+
+ y.<span class="me1">normal</span> <span class="sy0"><-</span> DGEList<span class="br0">(</span>counts <span class="sy0">=</span> counts, group <span class="sy0">=</span> group<span class="br0">)</span>
+
+ y.<span class="me1">normal</span><span class="br0">[</span>,<span class="nu0">1</span><span class="br0">]</span>
+
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/png.html"><span class="kw5">png</span></a><span class="br0">(</span>filename<span class="sy0">=</span>paste0<span class="br0">(</span>outdir,<span class="st0">"plots/"</span>,paste0<span class="br0">(</span>cName, <span class="st0">" edgeR - plotMDS"</span><span class="br0">)</span><span class="br0">)</span><span class="br0">)</span>
+ plotMDS<span class="br0">(</span>y.<span class="me1">normal</span>, method <span class="sy0">=</span> <span class="st0">"bcv"</span>, main <span class="sy0">=</span> paste0<span class="br0">(</span>cName, <span class="st0">"<span class="es0">\n</span>edgeR - plotMDS"</span><span class="br0">)</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/dev.off.html"><span class="kw5">dev.<span class="me1">off</span></span></a><span class="br0">(</span><span class="br0">)</span>
+
+ y.<span class="me1">normal</span> <span class="sy0"><-</span> calcNormFactors<span class="br0">(</span>y.<span class="me1">normal</span><span class="br0">)</span>
+ y.<span class="me1">normal</span> <span class="sy0"><-</span> estimateCommonDisp<span class="br0">(</span>y.<span class="me1">normal</span><span class="br0">)</span>
+ y.<span class="me1">normal</span> <span class="sy0"><-</span> estimateTagwiseDisp<span class="br0">(</span>y.<span class="me1">normal</span><span class="br0">)</span>
+
+
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/png.html"><span class="kw5">png</span></a><span class="br0">(</span>filename<span class="sy0">=</span>paste0<span class="br0">(</span>outdir,<span class="st0">"plots/"</span>,paste0<span class="br0">(</span>cName, <span class="st0">" edgeR - plotBCV"</span><span class="br0">)</span><span class="br0">)</span><span class="br0">)</span>
+ plotBCV<span class="br0">(</span>y.<span class="me1">normal</span>, main <span class="sy0">=</span> paste0<span class="br0">(</span>cName, <span class="st0">"<span class="es0">\n</span>edgeR - plotBCV"</span><span class="br0">)</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/dev.off.html"><span class="kw5">dev.<span class="me1">off</span></span></a><span class="br0">(</span><span class="br0">)</span>
+
+ et.<span class="me1">normal</span> <span class="sy0"><-</span> exactTest<span class="br0">(</span>y.<span class="me1">normal</span>, pair <span class="sy0">=</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span>sampleNameI, sampleNameII<span class="br0">)</span><span class="br0">)</span>
+
+ topTags<span class="br0">(</span>et.<span class="me1">normal</span><span class="br0">)</span>
+ <span class="co1"># adjust.method ==> character string specifying p-value adjustment method. Possible values are "none", "BH", "fdr" (equivalent to "BH"), "BY" and "holm". See p.adjust for details.</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/summary.html"><span class="kw2">summary</span></a><span class="br0">(</span>de.<span class="me1">normal</span> <span class="sy0"><-</span> decideTestsDGE<span class="br0">(</span>et.<span class="me1">normal</span>, p <span class="sy0">=</span> pvt, adjust <span class="sy0">=</span> <span class="st0">"BH"</span><span class="br0">)</span><span class="br0">)</span>
+ et.<span class="me1">normal</span>.<span class="me1">fdr</span> <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/cbind.html"><span class="kw2">cbind</span></a><span class="br0">(</span>et.<span class="me1">normal</span>$table, <a href="http://stat.ethz.ch/R-manual/R-devel/library/stats/html/p.adjust.html"><span class="kw7">p.<span class="me1">adjust</span></span></a><span class="br0">(</span>et.<span class="me1">normal</span>$table<span class="br0">[</span>, <span class="nu0">3</span><span class="br0">]</span>, method <span class="sy0">=</span> <span class="st0">"BH"</span><span class="br0">)</span><span class="br0">)</span>
+ et.<span class="me1">normal</span>.<span class="me1">fdr</span> <span class="sy0"><-</span> et.<span class="me1">normal</span>.<span class="me1">fdr</span><span class="br0">[</span>et.<span class="me1">normal</span>.<span class="me1">fdr</span><span class="br0">[</span>, <span class="nu0">4</span><span class="br0">]</span> <span class="sy0"><</span> pvt, <span class="br0">]</span>
+
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/write.table.html"><span class="kw8">write.<span class="me1">table</span></span></a><span class="br0">(</span>et.<span class="me1">normal</span>.<span class="me1">fdr</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/file.html"><span class="kw2">file</span></a> <span class="sy0">=</span> paste0<span class="br0">(</span>outdir, cName, <span class="st0">"_"</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/nrow.html"><span class="kw2">nrow</span></a><span class="br0">(</span>et.<span class="me1">normal</span>.<span class="me1">fdr</span><span class="br0">)</span>, <span class="st0">"_edgeR_fdr.tsv"</span><span class="br0">)</span>, sep <span class="sy0">=</span> <span class="st0">"<span class="es0">\t</span>"</span>, col.<span class="me1">names</span> <span class="sy0">=</span> TRUE, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/row.names.html"><span class="kw2">row.<span class="me1">names</span></span></a> <span class="sy0">=</span> TRUE, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/quote.html"><span class="kw2">quote</span></a> <span class="sy0">=</span> FALSE<span class="br0">)</span>
+
+ detags.<span class="me1">normal</span> <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/rownames.html"><span class="kw2">rownames</span></a><span class="br0">(</span>de.<span class="me1">normal</span><span class="br0">)</span><span class="br0">[</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/as.logical.html"><span class="kw2">as.<span class="me1">logical</span></span></a><span class="br0">(</span>de.<span class="me1">normal</span><span class="br0">)</span><span class="br0">]</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/png.html"><span class="kw5">png</span></a><span class="br0">(</span>filename<span class="sy0">=</span>paste0<span class="br0">(</span>outdir,<span class="st0">"plots/"</span>,paste0<span class="br0">(</span>cName, <span class="st0">" edgeR - plotSmear"</span><span class="br0">)</span><span class="br0">)</span><span class="br0">)</span>
+ plotSmear<span class="br0">(</span>et.<span class="me1">normal</span>, de.<span class="me1">normal</span>, tags <span class="sy0">=</span> detags.<span class="me1">normal</span>, main <span class="sy0">=</span> paste0<span class="br0">(</span>cName, <span class="st0">"<span class="es0">\n</span>edgeR - plotSmear"</span><span class="br0">)</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/graphics/html/abline.html"><span class="kw4">abline</span></a><span class="br0">(</span>h <span class="sy0">=</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span><span class="sy0">-</span><span class="nu0">2</span>, <span class="nu0">2</span><span class="br0">)</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/col.html"><span class="kw2">col</span></a> <span class="sy0">=</span> <span class="st0">"blue"</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/dev.off.html"><span class="kw5">dev.<span class="me1">off</span></span></a><span class="br0">(</span><span class="br0">)</span>
+
+ <span class="co1"># edgeR 'GLM'</span>
+
+ y.<span class="me1">glm</span> <span class="sy0"><-</span> DGEList<span class="br0">(</span>counts <span class="sy0">=</span> counts, group <span class="sy0">=</span> group<span class="br0">)</span>
+
+ design <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/stats/html/model.matrix.html"><span class="kw7">model.<span class="me1">matrix</span></span></a><span class="br0">(</span>~<span class="nu0">0</span> <span class="sy0">+</span> group, <a href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/data.html"><span class="kw8">data</span></a> <span class="sy0">=</span> y.<span class="me1">glm</span>$samples<span class="br0">)</span>
+ design
+
+ y.<span class="me1">glm</span> <span class="sy0"><-</span> estimateGLMCommonDisp<span class="br0">(</span>y.<span class="me1">glm</span>, design<span class="br0">)</span>
+ y.<span class="me1">glm</span> <span class="sy0"><-</span> estimateGLMTrendedDisp<span class="br0">(</span>y.<span class="me1">glm</span>, design<span class="br0">)</span>
+
+ <span class="co1">## Loading required package: splines</span>
+ y.<span class="me1">glm</span> <span class="sy0"><-</span> estimateGLMTagwiseDisp<span class="br0">(</span>y.<span class="me1">glm</span>, design<span class="br0">)</span>
+
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/png.html"><span class="kw5">png</span></a><span class="br0">(</span>filename<span class="sy0">=</span>paste0<span class="br0">(</span>outdir,<span class="st0">"plots/"</span>,paste0<span class="br0">(</span>cName, <span class="st0">" edgeR - plotBCV - GLM"</span><span class="br0">)</span><span class="br0">)</span><span class="br0">)</span>
+ plotBCV<span class="br0">(</span>y.<span class="me1">glm</span>, main <span class="sy0">=</span> paste0<span class="br0">(</span>cName, <span class="st0">"<span class="es0">\n</span>edgeR - plotBCV - GLM"</span><span class="br0">)</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/dev.off.html"><span class="kw5">dev.<span class="me1">off</span></span></a><span class="br0">(</span><span class="br0">)</span>
+
+ y.<span class="me1">fit</span> <span class="sy0"><-</span> glmFit<span class="br0">(</span>y.<span class="me1">glm</span>, design<span class="br0">)</span>
+ y.<span class="me1">lrt</span> <span class="sy0"><-</span> glmLRT<span class="br0">(</span>y.<span class="me1">fit</span><span class="br0">)</span>
+
+ FDR <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/stats/html/p.adjust.html"><span class="kw7">p.<span class="me1">adjust</span></span></a><span class="br0">(</span>y.<span class="me1">lrt</span>$table$PValue, method <span class="sy0">=</span> <span class="st0">"BH"</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/sum.html"><span class="kw2">sum</span></a><span class="br0">(</span>FDR <span class="sy0"><</span> pvt<span class="br0">)</span>
+
+ topTags<span class="br0">(</span>y.<span class="me1">lrt</span><span class="br0">)</span>
+
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/summary.html"><span class="kw2">summary</span></a><span class="br0">(</span>de.<span class="me1">glm</span> <span class="sy0"><-</span> decideTestsDGE<span class="br0">(</span>y.<span class="me1">lrt</span>, p <span class="sy0">=</span> pvt, adjust <span class="sy0">=</span> <span class="st0">"BH"</span><span class="br0">)</span><span class="br0">)</span>
+
+<span class="br0">}</span>
+
+
+DESeq2Function <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/function.html"><span class="kw2">function</span></a><span class="br0">(</span>odir, DESeq2Dir, cName, RTableInFiles, pvtDESeq2, sampleNameI, sampleNameII, sampleNameList<span class="br0">)</span>
+<span class="br0">{</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/library.html"><span class="kw2">library</span></a><span class="br0">(</span>DESeq2<span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/library.html"><span class="kw2">library</span></a><span class="br0">(</span>RColorBrewer<span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/library.html"><span class="kw2">library</span></a><span class="br0">(</span>gplots<span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/library.html"><span class="kw2">library</span></a><span class="br0">(</span>vsn<span class="br0">)</span>
+
+ outdir <span class="sy0"><-</span> paste0<span class="br0">(</span>odir, <span class="st0">"/"</span>,DESeq2Dir,<span class="st0">"/"</span><span class="br0">)</span> <span class="co1"># set outdir</span>
+
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/dir.create.html"><span class="kw2">dir.<span class="me1">create</span></span></a><span class="br0">(</span>outdir, showWarnings <span class="sy0">=</span> FALSE<span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/dir.create.html"><span class="kw2">dir.<span class="me1">create</span></span></a><span class="br0">(</span>paste0<span class="br0">(</span>outdir,<span class="st0">"plots"</span><span class="br0">)</span>, showWarnings <span class="sy0">=</span> FALSE<span class="br0">)</span> <span class="co1"># create subfolder "plots"</span>
+
+
+ pvt <span class="sy0"><-</span> pvtDESeq2
+
+
+
+ <span class="co1"># DESeqDataSet(se, design, ignoreRank = FALSE)</span>
+ <span class="co1"># DESeqDataSetFromMatrix(countData, colData, design, tidy = FALSE, ignoreRank = FALSE, ...)</span>
+ <span class="co1"># DESeqDataSetFromHTSeqCount(sampleTable, directory = ".", design, ignoreRank = FALSE, ...)</span>
+ <span class="co1"># DESeqDataSetFromTximport(txi, colData, design, ...)</span>
+ coldata <span class="sy0">=</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/data.frame.html"><span class="kw2">data.<span class="me1">frame</span></span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/row.names.html"><span class="kw2">row.<span class="me1">names</span></span></a> <span class="sy0">=</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/colnames.html"><span class="kw2">colnames</span></a><span class="br0">(</span>RTableInFiles<span class="br0">)</span>, condition <span class="sy0">=</span> sampleNameList<span class="br0">)</span>
+
+ ddsHTSeq <span class="sy0"><-</span> DESeqDataSetFromMatrix<span class="br0">(</span>countData <span class="sy0">=</span> RTableInFiles, colData <span class="sy0">=</span> coldata, design <span class="sy0">=</span> ~ condition<span class="br0">)</span>
+
+ colData<span class="br0">(</span>ddsHTSeq<span class="br0">)</span>$condition <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/factor.html"><span class="kw2">factor</span></a><span class="br0">(</span>colData<span class="br0">(</span>ddsHTSeq<span class="br0">)</span>$condition, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/levels.html"><span class="kw2">levels</span></a> <span class="sy0">=</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span>sampleNameI, sampleNameII<span class="br0">)</span><span class="br0">)</span>
+
+ ddsHTSeq <span class="sy0"><-</span> DESeq<span class="br0">(</span>ddsHTSeq<span class="br0">)</span>
+
+ ddsHTSeq.<span class="me1">res</span> <span class="sy0"><-</span> results<span class="br0">(</span>ddsHTSeq<span class="br0">)</span>
+ ddsHTSeq.<span class="me1">res</span> <span class="sy0"><-</span> ddsHTSeq.<span class="me1">res</span><span class="br0">[</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/order.html"><span class="kw2">order</span></a><span class="br0">(</span>ddsHTSeq.<span class="me1">res</span>$padj<span class="br0">)</span>, <span class="br0">]</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/head.html"><span class="kw8">head</span></a><span class="br0">(</span>ddsHTSeq.<span class="me1">res</span><span class="br0">)</span>
+
+ <span class="co1"># png(filename=paste0(outdir,"plots/",paste0(cName, " DESeq2 - plotMA")))</span>
+ <span class="co1"># plotMA(ddsHTSeq, main = paste0(cName, "\nDESeq2 - plotMA"), ylim = c(-2, 2))</span>
+ <span class="co1"># dev.off()</span>
+
+ ddsHTSeq.<span class="me1">res</span>.<span class="me1">fdr</span> <span class="sy0"><-</span> ddsHTSeq.<span class="me1">res</span><span class="br0">[</span><span class="sy0">!</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/is.na.html"><span class="kw2">is.<span class="me1">na</span></span></a><span class="br0">(</span>ddsHTSeq.<span class="me1">res</span>$padj<span class="br0">)</span>, <span class="br0">]</span>
+ ddsHTSeq.<span class="me1">res</span>.<span class="me1">fdr</span> <span class="sy0"><-</span> ddsHTSeq.<span class="me1">res</span>.<span class="me1">fdr</span><span class="br0">[</span>ddsHTSeq.<span class="me1">res</span>.<span class="me1">fdr</span>$padj <span class="sy0"><</span> pvt, <span class="br0">]</span>
+
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/write.table.html"><span class="kw8">write.<span class="me1">table</span></span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/as.matrix.html"><span class="kw2">as.<span class="me1">matrix</span></span></a><span class="br0">(</span>ddsHTSeq.<span class="me1">res</span>.<span class="me1">fdr</span><span class="br0">)</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/file.html"><span class="kw2">file</span></a> <span class="sy0">=</span> paste0<span class="br0">(</span>outdir, cName, <span class="st0">"_"</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/nrow.html"><span class="kw2">nrow</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/as.matrix.html"><span class="kw2">as.<span class="me1">matrix</span></span></a><span class="br0">(</span>ddsHTSeq.<span class="me1">res</span>.<span class="me1">fdr</span><span class="br0">)</span><span class="br0">)</span>, <span class="st0">"_DESeq2_fdr.tsv"</span><span class="br0">)</span>, sep <span class="sy0">=</span> <span class="st0">"<span class="es0">\t</span>"</span>, col.<span class="me1">names</span> <span class="sy0">=</span> TRUE, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/row.names.html"><span class="kw2">row.<span class="me1">names</span></span></a> <span class="sy0">=</span> TRUE, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/quote.html"><span class="kw2">quote</span></a> <span class="sy0">=</span> FALSE<span class="br0">)</span>
+
+ ddsHTSeq.<span class="me1">rld</span> <span class="sy0"><-</span> rlogTransformation<span class="br0">(</span>ddsHTSeq, blind <span class="sy0">=</span> TRUE<span class="br0">)</span>
+ ddsHTSeq.<span class="me1">vsd</span> <span class="sy0"><-</span> varianceStabilizingTransformation<span class="br0">(</span>ddsHTSeq, blind <span class="sy0">=</span> TRUE<span class="br0">)</span>
+
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/graphics/html/par.html"><span class="kw4">par</span></a><span class="br0">(</span>mfrow <span class="sy0">=</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span><span class="nu0">1</span>, <span class="nu0">3</span><span class="br0">)</span><span class="br0">)</span>
+ notAllZero <span class="sy0"><-</span> <span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/rowSums.html"><span class="kw2">rowSums</span></a><span class="br0">(</span>counts<span class="br0">(</span>ddsHTSeq<span class="br0">)</span><span class="br0">)</span> <span class="sy0">></span> <span class="nu0">0</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/png.html"><span class="kw5">png</span></a><span class="br0">(</span>filename<span class="sy0">=</span>paste0<span class="br0">(</span>outdir,<span class="st0">"plots/"</span>,paste0<span class="br0">(</span>cName, <span class="st0">" DESeq2 - SdPlot.1"</span><span class="br0">)</span><span class="br0">)</span><span class="br0">)</span>
+ meanSdPlot<span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/log2.html"><span class="kw2">log2</span></a><span class="br0">(</span>counts<span class="br0">(</span>ddsHTSeq, normalized <span class="sy0">=</span> TRUE<span class="br0">)</span><span class="br0">[</span>notAllZero, <span class="br0">]</span> <span class="sy0">+</span> <span class="nu0">1</span><span class="br0">)</span><span class="br0">)</span> <span class="co1"># , ylim = c(0, 2.5)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/dev.off.html"><span class="kw5">dev.<span class="me1">off</span></span></a><span class="br0">(</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/png.html"><span class="kw5">png</span></a><span class="br0">(</span>filename<span class="sy0">=</span>paste0<span class="br0">(</span>outdir,<span class="st0">"plots/"</span>,paste0<span class="br0">(</span>cName, <span class="st0">" DESeq2 - SdPlot.2"</span><span class="br0">)</span><span class="br0">)</span><span class="br0">)</span> <span class="co1"># , ylim = c(0, 2.5)</span>
+ meanSdPlot<span class="br0">(</span>assay<span class="br0">(</span>ddsHTSeq.<span class="me1">rld</span><span class="br0">[</span>notAllZero, <span class="br0">]</span><span class="br0">)</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/dev.off.html"><span class="kw5">dev.<span class="me1">off</span></span></a><span class="br0">(</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/png.html"><span class="kw5">png</span></a><span class="br0">(</span>filename<span class="sy0">=</span>paste0<span class="br0">(</span>outdir,<span class="st0">"plots/"</span>,paste0<span class="br0">(</span>cName, <span class="st0">" DESeq2 - SdPlot.3"</span><span class="br0">)</span><span class="br0">)</span><span class="br0">)</span> <span class="co1"># , ylim = c(0, 2.5)</span>
+ meanSdPlot<span class="br0">(</span>assay<span class="br0">(</span>ddsHTSeq.<span class="me1">vsd</span><span class="br0">[</span>notAllZero, <span class="br0">]</span><span class="br0">)</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/dev.off.html"><span class="kw5">dev.<span class="me1">off</span></span></a><span class="br0">(</span><span class="br0">)</span>
+
+ hmcol <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/colorRampPalette.html"><span class="kw5">colorRampPalette</span></a><span class="br0">(</span>brewer.<span class="me1">pal</span><span class="br0">(</span><span class="nu0">9</span>, <span class="st0">"GnBu"</span><span class="br0">)</span><span class="br0">)</span><span class="br0">(</span><span class="nu0">100</span><span class="br0">)</span>
+ distRL <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/stats/html/dist.html"><span class="kw7">dist</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/t.html"><span class="kw2">t</span></a><span class="br0">(</span>assay<span class="br0">(</span>ddsHTSeq.<span class="me1">rld</span><span class="br0">)</span><span class="br0">)</span><span class="br0">)</span>
+ mat <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/as.matrix.html"><span class="kw2">as.<span class="me1">matrix</span></span></a><span class="br0">(</span>distRL<span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/rownames.html"><span class="kw2">rownames</span></a><span class="br0">(</span>mat<span class="br0">)</span> <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/colnames.html"><span class="kw2">colnames</span></a><span class="br0">(</span>mat<span class="br0">)</span> <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/with.html"><span class="kw2">with</span></a><span class="br0">(</span>colData<span class="br0">(</span>ddsHTSeq<span class="br0">)</span>, paste0<span class="br0">(</span>condition<span class="br0">)</span><span class="br0">)</span>
+
+ <span class="co1"># png(filename=paste0(outdir,"plots/",paste0(cName, " DESeq2 - heatmap")))</span>
+ <span class="co1"># heatmap(mat, trace = "none", col = rev(hmcol), margin = c(13, 13))</span>
+ <span class="co1"># dev.off()</span>
+
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/png.html"><span class="kw5">png</span></a><span class="br0">(</span>filename<span class="sy0">=</span>paste0<span class="br0">(</span>outdir,<span class="st0">"plots/"</span>,paste0<span class="br0">(</span>cName, <span class="st0">" DESeq2 - PCA"</span><span class="br0">)</span><span class="br0">)</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span>plotPCA<span class="br0">(</span>ddsHTSeq.<span class="me1">rld</span>, intgroup <span class="sy0">=</span> <span class="st0">"condition"</span><span class="br0">)</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/dev.off.html"><span class="kw5">dev.<span class="me1">off</span></span></a><span class="br0">(</span><span class="br0">)</span>
+
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/png.html"><span class="kw5">png</span></a><span class="br0">(</span>filename<span class="sy0">=</span>paste0<span class="br0">(</span>outdir,<span class="st0">"plots/"</span>,paste0<span class="br0">(</span>cName, <span class="st0">" DESeq2 - DispEsts"</span><span class="br0">)</span><span class="br0">)</span><span class="br0">)</span>
+ plotDispEsts<span class="br0">(</span>ddsHTSeq, main <span class="sy0">=</span> paste0<span class="br0">(</span>cName, <span class="st0">"<span class="es0">\n</span>DESeq2 - plotDispEsts"</span><span class="br0">)</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/dev.off.html"><span class="kw5">dev.<span class="me1">off</span></span></a><span class="br0">(</span><span class="br0">)</span>
+<span class="br0">}</span>
+
+NOISeqFunction <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/function.html"><span class="kw2">function</span></a><span class="br0">(</span>odir, NOISeqDir, cName, RTableInFiles, pvtNOISeq, sampleNameI, sampleNameII, myLenPos, myGCPos, LenGCTable, columnPos, sampleNameList, SampleNames<span class="br0">)</span>
+<span class="br0">{</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/library.html"><span class="kw2">library</span></a><span class="br0">(</span>NOISeq<span class="br0">)</span>
+
+ outdir <span class="sy0"><-</span> paste0<span class="br0">(</span>odir, <span class="st0">"/"</span>,NOISeqDir,<span class="st0">"/"</span><span class="br0">)</span> <span class="co1"># set outdir</span>
+
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/dir.create.html"><span class="kw2">dir.<span class="me1">create</span></span></a><span class="br0">(</span>outdir, showWarnings <span class="sy0">=</span> FALSE<span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/dir.create.html"><span class="kw2">dir.<span class="me1">create</span></span></a><span class="br0">(</span>paste0<span class="br0">(</span>outdir,<span class="st0">"plots"</span><span class="br0">)</span>, showWarnings <span class="sy0">=</span> FALSE<span class="br0">)</span> <span class="co1"># create subfolder "plots"</span>
+
+ pvt <span class="sy0"><-</span> pvtNOISeq
+
+ counts <span class="sy0"><-</span> RTableInFiles<span class="br0">[</span>, columnPos<span class="br0">]</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/head.html"><span class="kw8">head</span></a><span class="br0">(</span>counts<span class="br0">)</span>
+
+ <span class="co1"># must be changed if there are no triplicates</span>
+ <span class="co1"># !! Please change this setting if needed !!</span>
+ myfactors <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/data.frame.html"><span class="kw2">data.<span class="me1">frame</span></span></a><span class="br0">(</span>Treatment <span class="sy0">=</span> sampleNameList, TreatmentRun <span class="sy0">=</span> SampleNames<span class="br0">)</span>
+ <span class="co1"># sort counts by row names</span>
+ mycounts <span class="sy0"><-</span> counts<span class="br0">[</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/order.html"><span class="kw2">order</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/rownames.html"><span class="kw2">rownames</span></a><span class="br0">(</span>counts<span class="br0">)</span><span class="br0">)</span>, <span class="br0">]</span>
+ <span class="co1"># filter out low counts</span>
+ mycounts.<span class="me1">filter</span> <span class="sy0"><-</span> filtered.<span class="me1">data</span><span class="br0">(</span>mycounts, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/factor.html"><span class="kw2">factor</span></a> <span class="sy0">=</span> myfactors$Treatment, norm <span class="sy0">=</span> FALSE, depth <span class="sy0">=</span> NULL, method <span class="sy0">=</span> <span class="nu0">1</span>, cv.<span class="me1">cutoff</span> <span class="sy0">=</span> <span class="nu0">100</span>, cpm <span class="sy0">=</span> <span class="nu0">1</span><span class="br0">)</span>
+ mycounts.<span class="me1">rowname</span> <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/rownames.html"><span class="kw2">rownames</span></a><span class="br0">(</span>mycounts.<span class="me1">filter</span><span class="br0">)</span>
+
+ <span class="co1"># Extra file with length and GC content</span>
+ myLengthTable <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/read.table.html"><span class="kw8">read.<span class="me1">table</span></span></a><span class="br0">(</span>LenGCTable, sep <span class="sy0">=</span> <span class="st0">"<span class="es0">\t</span>"</span>, header <span class="sy0">=</span> TRUE, stringsAsFactor <span class="sy0">=</span> FALSE, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/row.names.html"><span class="kw2">row.<span class="me1">names</span></span></a><span class="sy0">=</span><span class="nu0">1</span><span class="br0">)</span>
+ myLengthTable <span class="sy0"><-</span> myLengthTable<span class="br0">[</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/order.html"><span class="kw2">order</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/rownames.html"><span class="kw2">rownames</span></a><span class="br0">(</span>myLengthTable<span class="br0">)</span><span class="br0">)</span>,<span class="br0">]</span> <span class="co1"># sort by rownames</span>
+ myLengthTable.<span class="me1">filter</span> <span class="sy0"><-</span> myLengthTable<span class="br0">[</span>mycounts.<span class="me1">rowname</span>,<span class="br0">]</span>
+
+ mylength <span class="sy0"><-</span> myLengthTable.<span class="me1">filter</span><span class="br0">[</span>,myLenPos<span class="br0">]</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/names.html"><span class="kw2">names</span></a><span class="br0">(</span>mylength<span class="br0">)</span> <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/rownames.html"><span class="kw2">rownames</span></a><span class="br0">(</span>myLengthTable.<span class="me1">filter</span><span class="br0">)</span>
+
+ mygc <span class="sy0"><-</span> myLengthTable.<span class="me1">filter</span><span class="br0">[</span>,myGCPos<span class="br0">]</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/names.html"><span class="kw2">names</span></a><span class="br0">(</span>mygc<span class="br0">)</span> <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/rownames.html"><span class="kw2">rownames</span></a><span class="br0">(</span>myLengthTable.<span class="me1">filter</span><span class="br0">)</span>
+
+
+
+
+
+ mydata <span class="sy0"><-</span> readData<span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/data.html"><span class="kw8">data</span></a> <span class="sy0">=</span> mycounts.<span class="me1">filter</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/length.html"><span class="kw2">length</span></a> <span class="sy0">=</span> mylength, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/gc.html"><span class="kw2">gc</span></a> <span class="sy0">=</span> mygc, factors <span class="sy0">=</span> myfactors<span class="br0">)</span>
+ mydata
+
+ mydata.<span class="me1">GCbias</span> <span class="sy0"><-</span> dat<span class="br0">(</span>mydata, type <span class="sy0">=</span> <span class="st0">"GCbias"</span><span class="br0">)</span>
+<span class="co1">#-# png(filename=paste0(outdir,"plots/",paste0(cName, " NOISeq - GCbias.1")))</span>
+<span class="co1">#-# explo.plot(mydata.GCbias)</span>
+<span class="co1">#-# dev.off()</span>
+
+ mydata.<span class="me1">GCbias</span>.<span class="me1">group</span> <span class="sy0"><-</span> dat<span class="br0">(</span>mydata, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/factor.html"><span class="kw2">factor</span></a> <span class="sy0">=</span> <span class="st0">"Treatment"</span>, type <span class="sy0">=</span> <span class="st0">"GCbias"</span><span class="br0">)</span>
+<span class="co1">#-# png(filename=paste0(outdir,"plots/",paste0(cName, " NOISeq - GCbias.2")))</span>
+<span class="co1">#-# explo.plot(mydata.GCbias.group)</span>
+<span class="co1">#-# dev.off()</span>
+
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/methods/html/show.html"><span class="kw6">show</span></a><span class="br0">(</span>mydata.<span class="me1">GCbias</span>.<span class="me1">group</span><span class="br0">)</span>
+
+ mydata.<span class="me1">lengthbias</span> <span class="sy0"><-</span> dat<span class="br0">(</span>mydata, type <span class="sy0">=</span> <span class="st0">"lengthbias"</span><span class="br0">)</span>
+<span class="co1">#-# png(filename=paste0(outdir,"plots/",paste0(cName, " NOISeq - Lenbias.1")))</span>
+<span class="co1">#-# explo.plot(mydata.lengthbias)</span>
+<span class="co1">#-# dev.off()</span>
+
+ mydata.<span class="me1">lengthbias</span>.<span class="me1">group</span> <span class="sy0"><-</span> dat<span class="br0">(</span>mydata, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/factor.html"><span class="kw2">factor</span></a> <span class="sy0">=</span> <span class="st0">"Treatment"</span>, type <span class="sy0">=</span> <span class="st0">"lengthbias"</span><span class="br0">)</span>
+<span class="co1">#-# png(filename=paste0(outdir,"plots/",paste0(cName, " NOISeq - Lenbias.2")))</span>
+<span class="co1">#-# explo.plot(mydata.lengthbias.group)</span>
+<span class="co1">#-# dev.off()</span>
+
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/methods/html/show.html"><span class="kw6">show</span></a><span class="br0">(</span>mydata.<span class="me1">lengthbias</span>.<span class="me1">group</span><span class="br0">)</span>
+
+ <span class="co1"># looks different</span>
+ mydata.<span class="me1">cd</span> <span class="sy0"><-</span> dat<span class="br0">(</span>mydata, type <span class="sy0">=</span> <span class="st0">"cd"</span><span class="br0">)</span>
+<span class="co1">#-# png(filename=paste0(outdir,"plots/",paste0(cName, " NOISeq - cd")))</span>
+<span class="co1">#-# explo.plot(mydata.cd)</span>
+<span class="co1">#-# dev.off()</span>
+ mylength
+
+ myRPKM <span class="sy0"><-</span> NOISeq<span class="sy0">::</span><span class="me2">rpkm</span><span class="br0">(</span>assayData<span class="br0">(</span>mydata<span class="br0">)</span>$exprs<span class="br0">)</span>
+ myUQUA <span class="sy0"><-</span> NOISeq<span class="sy0">::</span><span class="me2">uqua</span><span class="br0">(</span>assayData<span class="br0">(</span>mydata<span class="br0">)</span>$exprs, long <span class="sy0">=</span> mylength, lc <span class="sy0">=</span> <span class="nu0">0.5</span>, k <span class="sy0">=</span> <span class="nu0">0</span><span class="br0">)</span>
+ myTMM <span class="sy0"><-</span> NOISeq<span class="sy0">::</span><span class="me2">tmm</span><span class="br0">(</span>assayData<span class="br0">(</span>mydata<span class="br0">)</span>$exprs, long <span class="sy0">=</span> <span class="nu0">1000</span>, lc <span class="sy0">=</span> <span class="nu0">0</span><span class="br0">)</span>
+
+ mynoiseq.<span class="me1">rpkm</span> <span class="sy0"><-</span> noiseq<span class="br0">(</span>mydata, k <span class="sy0">=</span> <span class="nu0">0.5</span>, norm <span class="sy0">=</span> <span class="st0">"rpkm"</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/factor.html"><span class="kw2">factor</span></a> <span class="sy0">=</span> <span class="st0">"Treatment"</span>, pnr <span class="sy0">=</span> <span class="nu0">0.2</span>, nss <span class="sy0">=</span> <span class="nu0">5</span>, v <span class="sy0">=</span> <span class="nu0">0.02</span>, lc <span class="sy0">=</span> <span class="nu0">1</span>, replicates <span class="sy0">=</span> <span class="st0">"biological"</span><span class="br0">)</span>
+ mynoiseq.<span class="me1">nnorm</span> <span class="sy0"><-</span> noiseq<span class="br0">(</span>mydata, k <span class="sy0">=</span> <span class="nu0">0.5</span>, norm <span class="sy0">=</span> <span class="st0">"n"</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/factor.html"><span class="kw2">factor</span></a> <span class="sy0">=</span> <span class="st0">"Treatment"</span>, pnr <span class="sy0">=</span> <span class="nu0">0.2</span>, nss <span class="sy0">=</span> <span class="nu0">5</span>, v <span class="sy0">=</span> <span class="nu0">0.02</span>, lc <span class="sy0">=</span> <span class="nu0">1</span>, replicates <span class="sy0">=</span> <span class="st0">"biological"</span><span class="br0">)</span>
+ mynoiseq.<span class="me1">tmm</span> <span class="sy0"><-</span> noiseq<span class="br0">(</span>mydata, k <span class="sy0">=</span> <span class="nu0">0.5</span>, norm <span class="sy0">=</span> <span class="st0">"tmm"</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/factor.html"><span class="kw2">factor</span></a> <span class="sy0">=</span> <span class="st0">"Treatment"</span>, pnr <span class="sy0">=</span> <span class="nu0">0.2</span>, nss <span class="sy0">=</span> <span class="nu0">5</span>, v <span class="sy0">=</span> <span class="nu0">0.02</span>, lc <span class="sy0">=</span> <span class="nu0">1</span>, replicates <span class="sy0">=</span> <span class="st0">"biological"</span><span class="br0">)</span>
+
+ <span class="co1"># RPKM</span>
+ mynoiseq.<span class="me1">rpkm</span>.<span class="me1">prob</span> <span class="sy0"><-</span> mynoiseq.<span class="me1">rpkm</span>@results<span class="br0">[</span><span class="br0">[</span><span class="nu0">1</span><span class="br0">]</span><span class="br0">]</span><span class="br0">[</span>mynoiseq.<span class="me1">rpkm</span>@results<span class="br0">[</span><span class="br0">[</span><span class="nu0">1</span><span class="br0">]</span><span class="br0">]</span>$prob <span class="sy0">></span> pvt, <span class="br0">]</span>
+ mynoiseq.<span class="me1">rpkm</span>.<span class="me1">prob</span> <span class="sy0"><-</span> mynoiseq.<span class="me1">rpkm</span>.<span class="me1">prob</span><span class="br0">[</span><span class="sy0">!</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/is.na.html"><span class="kw2">is.<span class="me1">na</span></span></a><span class="br0">(</span>mynoiseq.<span class="me1">rpkm</span>.<span class="me1">prob</span>$prob<span class="br0">)</span>, <span class="br0">]</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/write.table.html"><span class="kw8">write.<span class="me1">table</span></span></a><span class="br0">(</span>mynoiseq.<span class="me1">rpkm</span>.<span class="me1">prob</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/file.html"><span class="kw2">file</span></a> <span class="sy0">=</span> paste0<span class="br0">(</span>outdir, cName, <span class="st0">"_"</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/nrow.html"><span class="kw2">nrow</span></a><span class="br0">(</span>mynoiseq.<span class="me1">rpkm</span>.<span class="me1">prob</span><span class="br0">)</span>, <span class="st0">"_NOISeq_rpkm_prob.tsv"</span><span class="br0">)</span>, sep <span class="sy0">=</span> <span class="st0">"<span class="es0">\t</span>"</span>, col.<span class="me1">names</span> <span class="sy0">=</span> TRUE, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/row.names.html"><span class="kw2">row.<span class="me1">names</span></span></a> <span class="sy0">=</span> TRUE, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/quote.html"><span class="kw2">quote</span></a> <span class="sy0">=</span> FALSE<span class="br0">)</span>
+ <span class="co1"># none</span>
+ mynoiseq.<span class="me1">nnorm</span>.<span class="me1">prob</span> <span class="sy0"><-</span> mynoiseq.<span class="me1">nnorm</span>@results<span class="br0">[</span><span class="br0">[</span><span class="nu0">1</span><span class="br0">]</span><span class="br0">]</span><span class="br0">[</span>mynoiseq.<span class="me1">nnorm</span>@results<span class="br0">[</span><span class="br0">[</span><span class="nu0">1</span><span class="br0">]</span><span class="br0">]</span>$prob <span class="sy0">></span> pvt, <span class="br0">]</span>
+ mynoiseq.<span class="me1">nnorm</span>.<span class="me1">prob</span> <span class="sy0"><-</span> mynoiseq.<span class="me1">nnorm</span>.<span class="me1">prob</span><span class="br0">[</span><span class="sy0">!</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/is.na.html"><span class="kw2">is.<span class="me1">na</span></span></a><span class="br0">(</span>mynoiseq.<span class="me1">nnorm</span>.<span class="me1">prob</span>$prob<span class="br0">)</span>, <span class="br0">]</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/write.table.html"><span class="kw8">write.<span class="me1">table</span></span></a><span class="br0">(</span>mynoiseq.<span class="me1">nnorm</span>.<span class="me1">prob</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/file.html"><span class="kw2">file</span></a> <span class="sy0">=</span> paste0<span class="br0">(</span>outdir, cName,<span class="st0">"_"</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/nrow.html"><span class="kw2">nrow</span></a><span class="br0">(</span>mynoiseq.<span class="me1">nnorm</span>.<span class="me1">prob</span><span class="br0">)</span>, <span class="st0">"_NOISeq_nnorm_prob.tsv"</span><span class="br0">)</span>, sep <span class="sy0">=</span> <span class="st0">"<span class="es0">\t</span>"</span>, col.<span class="me1">names</span> <span class="sy0">=</span> TRUE, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/row.names.html"><span class="kw2">row.<span class="me1">names</span></span></a> <span class="sy0">=</span> TRUE, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/quote.html"><span class="kw2">quote</span></a> <span class="sy0">=</span> FALSE<span class="br0">)</span>
+ <span class="co1"># TMM</span>
+ mynoiseq.<span class="me1">tmm</span>.<span class="me1">prob</span> <span class="sy0"><-</span> mynoiseq.<span class="me1">tmm</span>@results<span class="br0">[</span><span class="br0">[</span><span class="nu0">1</span><span class="br0">]</span><span class="br0">]</span><span class="br0">[</span>mynoiseq.<span class="me1">tmm</span>@results<span class="br0">[</span><span class="br0">[</span><span class="nu0">1</span><span class="br0">]</span><span class="br0">]</span>$prob <span class="sy0">></span> pvt, <span class="br0">]</span>
+ mynoiseq.<span class="me1">tmm</span>.<span class="me1">prob</span> <span class="sy0"><-</span> mynoiseq.<span class="me1">tmm</span>.<span class="me1">prob</span><span class="br0">[</span><span class="sy0">!</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/is.na.html"><span class="kw2">is.<span class="me1">na</span></span></a><span class="br0">(</span>mynoiseq.<span class="me1">tmm</span>.<span class="me1">prob</span>$prob<span class="br0">)</span>, <span class="br0">]</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/write.table.html"><span class="kw8">write.<span class="me1">table</span></span></a><span class="br0">(</span>mynoiseq.<span class="me1">tmm</span>.<span class="me1">prob</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/file.html"><span class="kw2">file</span></a> <span class="sy0">=</span> paste0<span class="br0">(</span>outdir, cName,<span class="st0">"_"</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/nrow.html"><span class="kw2">nrow</span></a><span class="br0">(</span>mynoiseq.<span class="me1">tmm</span>.<span class="me1">prob</span><span class="br0">)</span>, <span class="st0">"_NOISeq_tmm_prob.tsv"</span><span class="br0">)</span>, sep <span class="sy0">=</span> <span class="st0">"<span class="es0">\t</span>"</span>, col.<span class="me1">names</span> <span class="sy0">=</span> TRUE, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/row.names.html"><span class="kw2">row.<span class="me1">names</span></span></a> <span class="sy0">=</span> TRUE, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/quote.html"><span class="kw2">quote</span></a> <span class="sy0">=</span> FALSE<span class="br0">)</span>
+
+ <span class="co1">############ NOISeq bio ################</span>
+
+ pvtnsb <span class="sy0"><-</span> <span class="nu0">0.995</span>
+ a0per_value <span class="sy0"><-</span> <span class="nu0">0.99</span>
+
+ iterations <span class="sy0"><-</span> <span class="nu0">5</span>
+ x5 <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/sample.html"><span class="kw2">sample</span></a><span class="br0">(</span><span class="nu0">10000</span><span class="sy0">:</span><span class="nu0">99999</span>, iterations, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/replace.html"><span class="kw2">replace</span></a><span class="sy0">=</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/F.html"><span class="kw2">F</span></a><span class="br0">)</span>, <span class="nu0">12345</span><span class="br0">)</span>
+ x5
+
+ collector.<span class="me1">rpkm</span> <span class="sy0"><-</span> NULL
+ collector.<span class="me1">tmm</span> <span class="sy0"><-</span> NULL
+
+
+ <span class="co1"># for (iter in x5) {</span>
+ <span class="co1"># # RPKM</span>
+ <span class="co1"># mynoiseqbio.rpkm <- noiseqbio(mydata, k = 0.5, norm = "rpkm", factor = "Treatment", lc = 1, r = 20, adj = 1.5, a0per = a0per_value, random.seed = iter, filter = 1)#, plot = TRUE)</span>
+ <span class="co1"># mynoiseqbio.rpkm.prob <- mynoiseqbio.rpkm@results[[1]][mynoiseqbio.rpkm@results[[1]]$prob > pvtnsb, ]</span>
+ <span class="co1"># mynoiseqbio.rpkm.prob <- mynoiseqbio.rpkm.prob[!is.na(mynoiseqbio.rpkm.prob$prob), ]</span>
+ <span class="co1"># collector.rpkm <- rbind(collector.rpkm, mynoiseqbio.rpkm.prob)</span>
+ <span class="co1"># #collector <- rbind(collector, mynoiseqbio.rpkm.prob[rownames(mynoiseqbio.rpkm.prob) %in% rownames(collector),])</span>
+ <span class="co1"># # TMM</span>
+ <span class="co1"># mynoiseqbio.tmm <- noiseqbio(mydata, k = 0.5, norm = "tmm", factor = "Treatment", lc = 1, r = 20, adj = 1.5, a0per = a0per_value, random.seed = iter, filter = 1)#, plot = TRUE)</span>
+ <span class="co1"># mynoiseqbio.tmm.prob <- mynoiseqbio.tmm@results[[1]][mynoiseqbio.tmm@results[[1]]$prob > pvtnsb, ]</span>
+ <span class="co1"># mynoiseqbio.tmm.prob <- mynoiseqbio.tmm.prob[!is.na(mynoiseqbio.tmm.prob$prob), ]</span>
+ <span class="co1"># collector.tmm <- rbind(collector.tmm, mynoiseqbio.tmm.prob)</span>
+ <span class="co1"># }</span>
+ <span class="co1">#</span>
+ <span class="co1"># # RPKM</span>
+ <span class="co1"># print(sort(row.names(collector.rpkm)))</span>
+ <span class="co1"># library(stringr)</span>
+ <span class="co1"># mynoiseqbio.rpkm.prob.overlap <- collector.rpkm[str_split_fixed(row.names(collector.rpkm), "\\.",2)[,2]>=iterations+10,]</span>
+ <span class="co1"># row.names(mynoiseqbio.rpkm.prob.overlap) <- substr(row.names(mynoiseqbio.rpkm.prob.overlap),1,str_length(row.names(mynoiseqbio.rpkm.prob.overlap))-1)</span>
+ <span class="co1">#</span>
+ <span class="co1"># write.table(mynoiseqbio.rpkm.prob.overlap, file = paste0(outdir, cName,"_", nrow(mynoiseqbio.rpkm.prob.overlap),"_NOISeqbio_rpkm_prob_seed_iteration_overlap.tsv"), sep = "\t", col.names = TRUE, row.names = TRUE, quote = FALSE)</span>
+ <span class="co1">#</span>
+ <span class="co1"># #TMM</span>
+ <span class="co1"># print(sort(row.names(collector.tmm)))</span>
+ <span class="co1"># library(stringr)</span>
+ <span class="co1"># mynoiseqbio.tmm.prob.overlap <- collector.tmm[str_split_fixed(row.names(collector.tmm), "\\.",2)[,2]>=iterations+10,]</span>
+ <span class="co1"># row.names(mynoiseqbio.tmm.prob.overlap) <- substr(row.names(mynoiseqbio.tmm.prob.overlap),1,str_length(row.names(mynoiseqbio.tmm.prob.overlap))-1)</span>
+ <span class="co1">#</span>
+ <span class="co1"># write.table(mynoiseqbio.tmm.prob.overlap, file = paste0(outdir, cName,"_", nrow(mynoiseqbio.tmm.prob.overlap),"_NOISeqbio_tmm_prob_seed_iteration_overlap.tsv"), sep = "\t", col.names = TRUE, row.names = TRUE, quote = FALSE)</span>
+
+ <span class="co1"># # none</span>
+ <span class="co1"># mynoiseqbio.nnorm.prob <- mynoiseqbio.nnorm@results[[1]][mynoiseqbio.nnorm@results[[1]]$prob > pvtnsb, ]</span>
+ <span class="co1"># mynoiseqbio.nnorm.prob <- mynoiseqbio.nnorm.prob[!is.na(mynoiseqbio.nnorm.prob$prob), ]</span>
+ <span class="co1"># write.table(mynoiseqbio.nnorm.prob, file = paste0(outdir, cName, "_NOISeqbio_nnorm_prob.tsv"), sep = "\t", col.names = TRUE, row.names = TRUE, quote = FALSE)</span>
+ <span class="co1"># # TMM</span>
+ <span class="co1"># mynoiseqbio.tmm.prob <- mynoiseqbio.tmm@results[[1]][mynoiseqbio.tmm@results[[1]]$prob > pvtnsb, ]</span>
+ <span class="co1"># mynoiseqbio.tmm.prob <- mynoiseqbio.tmm.prob[!is.na(mynoiseqbio.tmm.prob$prob), ]</span>
+ <span class="co1"># write.table(mynoiseqbio.tmm.prob, file = paste0(outdir, cName, "_NOISeqbio_tmm_prob.tsv"), sep = "\t", col.names = TRUE, row.names = TRUE, quote = FALSE)</span>
+
+
+
+
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/png.html"><span class="kw5">png</span></a><span class="br0">(</span>filename<span class="sy0">=</span>paste0<span class="br0">(</span>outdir,<span class="st0">"plots/"</span>,paste0<span class="br0">(</span>cName, <span class="st0">" NOISeq - noiseqbiorpkm"</span><span class="br0">)</span><span class="br0">)</span><span class="br0">)</span>
+ mynoiseqbio.<span class="me1">rpkm</span> <span class="sy0"><-</span> noiseqbio<span class="br0">(</span>mydata, k <span class="sy0">=</span> <span class="nu0">0.5</span>, norm <span class="sy0">=</span> <span class="st0">"rpkm"</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/factor.html"><span class="kw2">factor</span></a> <span class="sy0">=</span> <span class="st0">"Treatment"</span>, lc <span class="sy0">=</span> <span class="nu0">1</span>, r <span class="sy0">=</span> <span class="nu0">20</span>, adj <span class="sy0">=</span> <span class="nu0">1.5</span>, a0per <span class="sy0">=</span> a0per_value, random.<span class="me1">seed</span> <span class="sy0">=</span> <span class="nu0">12345</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/stats/html/filter.html"><span class="kw7">filter</span></a> <span class="sy0">=</span> <span class="nu0">1</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/graphics/html/plot.html"><span class="kw4">plot</span></a> <span class="sy0">=</span> TRUE<span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/dev.off.html"><span class="kw5">dev.<span class="me1">off</span></span></a><span class="br0">(</span><span class="br0">)</span>
+
+ mynoiseqbio.<span class="me1">rpkm</span>.<span class="me1">prob</span> <span class="sy0"><-</span> mynoiseqbio.<span class="me1">rpkm</span>@results<span class="br0">[</span><span class="br0">[</span><span class="nu0">1</span><span class="br0">]</span><span class="br0">]</span><span class="br0">[</span>mynoiseqbio.<span class="me1">rpkm</span>@results<span class="br0">[</span><span class="br0">[</span><span class="nu0">1</span><span class="br0">]</span><span class="br0">]</span>$prob <span class="sy0">></span> pvtnsb, <span class="br0">]</span>
+ mynoiseqbio.<span class="me1">rpkm</span>.<span class="me1">prob</span> <span class="sy0"><-</span> mynoiseqbio.<span class="me1">rpkm</span>.<span class="me1">prob</span><span class="br0">[</span><span class="sy0">!</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/is.na.html"><span class="kw2">is.<span class="me1">na</span></span></a><span class="br0">(</span>mynoiseqbio.<span class="me1">rpkm</span>.<span class="me1">prob</span>$prob<span class="br0">)</span>, <span class="br0">]</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/write.table.html"><span class="kw8">write.<span class="me1">table</span></span></a><span class="br0">(</span>mynoiseqbio.<span class="me1">rpkm</span>.<span class="me1">prob</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/file.html"><span class="kw2">file</span></a> <span class="sy0">=</span> paste0<span class="br0">(</span>outdir, cName,<span class="st0">"_"</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/nrow.html"><span class="kw2">nrow</span></a><span class="br0">(</span>mynoiseqbio.<span class="me1">rpkm</span>.<span class="me1">prob</span><span class="br0">)</span>,<span class="st0">"_NOISeqbio_rpkm_prob_seed_12345.tsv"</span><span class="br0">)</span>, sep <span class="sy0">=</span> <span class="st0">"<span class="es0">\t</span>"</span>, col.<span class="me1">names</span> <span class="sy0">=</span> TRUE, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/row.names.html"><span class="kw2">row.<span class="me1">names</span></span></a> <span class="sy0">=</span> TRUE, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/quote.html"><span class="kw2">quote</span></a> <span class="sy0">=</span> FALSE<span class="br0">)</span>
+
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/png.html"><span class="kw5">png</span></a><span class="br0">(</span>filename<span class="sy0">=</span>paste0<span class="br0">(</span>outdir,<span class="st0">"plots/"</span>,paste0<span class="br0">(</span>cName, <span class="st0">" NOISeq - noiseqbiontmm"</span><span class="br0">)</span><span class="br0">)</span><span class="br0">)</span>
+ mynoiseqbio.<span class="me1">tmm</span> <span class="sy0"><-</span> noiseqbio<span class="br0">(</span>mydata, k <span class="sy0">=</span> <span class="nu0">0.5</span>, norm <span class="sy0">=</span> <span class="st0">"tmm"</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/factor.html"><span class="kw2">factor</span></a> <span class="sy0">=</span> <span class="st0">"Treatment"</span>, lc <span class="sy0">=</span> <span class="nu0">1</span>, r <span class="sy0">=</span> <span class="nu0">20</span>, adj <span class="sy0">=</span> <span class="nu0">1.5</span>, a0per <span class="sy0">=</span> a0per_value, random.<span class="me1">seed</span> <span class="sy0">=</span> <span class="nu0">12345</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/stats/html/filter.html"><span class="kw7">filter</span></a> <span class="sy0">=</span> <span class="nu0">1</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/graphics/html/plot.html"><span class="kw4">plot</span></a> <span class="sy0">=</span> TRUE<span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/dev.off.html"><span class="kw5">dev.<span class="me1">off</span></span></a><span class="br0">(</span><span class="br0">)</span>
+
+ mynoiseqbio.<span class="me1">tmm</span>.<span class="me1">prob</span> <span class="sy0"><-</span> mynoiseqbio.<span class="me1">tmm</span>@results<span class="br0">[</span><span class="br0">[</span><span class="nu0">1</span><span class="br0">]</span><span class="br0">]</span><span class="br0">[</span>mynoiseqbio.<span class="me1">tmm</span>@results<span class="br0">[</span><span class="br0">[</span><span class="nu0">1</span><span class="br0">]</span><span class="br0">]</span>$prob <span class="sy0">></span> pvtnsb, <span class="br0">]</span>
+ mynoiseqbio.<span class="me1">tmm</span>.<span class="me1">prob</span> <span class="sy0"><-</span> mynoiseqbio.<span class="me1">tmm</span>.<span class="me1">prob</span><span class="br0">[</span><span class="sy0">!</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/is.na.html"><span class="kw2">is.<span class="me1">na</span></span></a><span class="br0">(</span>mynoiseqbio.<span class="me1">tmm</span>.<span class="me1">prob</span>$prob<span class="br0">)</span>, <span class="br0">]</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/write.table.html"><span class="kw8">write.<span class="me1">table</span></span></a><span class="br0">(</span>mynoiseqbio.<span class="me1">tmm</span>.<span class="me1">prob</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/file.html"><span class="kw2">file</span></a> <span class="sy0">=</span> paste0<span class="br0">(</span>outdir, cName,<span class="st0">"_"</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/nrow.html"><span class="kw2">nrow</span></a><span class="br0">(</span>mynoiseqbio.<span class="me1">tmm</span>.<span class="me1">prob</span><span class="br0">)</span>,<span class="st0">"_NOISeqbio_tmm_prob_seed_12345.tsv"</span><span class="br0">)</span>, sep <span class="sy0">=</span> <span class="st0">"<span class="es0">\t</span>"</span>, col.<span class="me1">names</span> <span class="sy0">=</span> TRUE, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/row.names.html"><span class="kw2">row.<span class="me1">names</span></span></a> <span class="sy0">=</span> TRUE, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/quote.html"><span class="kw2">quote</span></a> <span class="sy0">=</span> FALSE<span class="br0">)</span>
+
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/png.html"><span class="kw5">png</span></a><span class="br0">(</span>filename<span class="sy0">=</span>paste0<span class="br0">(</span>outdir,<span class="st0">"plots/"</span>,paste0<span class="br0">(</span>cName, <span class="st0">" NOISeq - noiseqbionnorm"</span><span class="br0">)</span><span class="br0">)</span><span class="br0">)</span>
+ mynoiseqbio.<span class="me1">nnorm</span> <span class="sy0"><-</span> noiseqbio<span class="br0">(</span>mydata, k <span class="sy0">=</span> <span class="nu0">0.5</span>, norm <span class="sy0">=</span> <span class="st0">"n"</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/factor.html"><span class="kw2">factor</span></a> <span class="sy0">=</span> <span class="st0">"Treatment"</span>, lc <span class="sy0">=</span> <span class="nu0">1</span>, r <span class="sy0">=</span> <span class="nu0">20</span>, adj <span class="sy0">=</span> <span class="nu0">1.5</span>, a0per <span class="sy0">=</span> a0per_value, random.<span class="me1">seed</span> <span class="sy0">=</span> <span class="nu0">12345</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/stats/html/filter.html"><span class="kw7">filter</span></a> <span class="sy0">=</span> <span class="nu0">1</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/graphics/html/plot.html"><span class="kw4">plot</span></a> <span class="sy0">=</span> TRUE<span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/dev.off.html"><span class="kw5">dev.<span class="me1">off</span></span></a><span class="br0">(</span><span class="br0">)</span>
+
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/head.html"><span class="kw8">head</span></a><span class="br0">(</span>mynoiseqbio.<span class="me1">rpkm</span>@results<span class="br0">[</span><span class="br0">[</span><span class="nu0">1</span><span class="br0">]</span><span class="br0">]</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/head.html"><span class="kw8">head</span></a><span class="br0">(</span>mynoiseqbio.<span class="me1">nnorm</span>@results<span class="br0">[</span><span class="br0">[</span><span class="nu0">1</span><span class="br0">]</span><span class="br0">]</span><span class="br0">)</span>
+
+ mynoiseqbio.<span class="me1">rpkm</span>.<span class="me1">deg</span> <span class="sy0"><-</span> degenes<span class="br0">(</span>mynoiseqbio.<span class="me1">rpkm</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/q.html"><span class="kw2">q</span></a> <span class="sy0">=</span> pvtnsb, M <span class="sy0">=</span> NULL<span class="br0">)</span>
+
+ mynoiseqbio.<span class="me1">rpkm</span>.<span class="me1">deg</span>.<span class="me1">up</span> <span class="sy0"><-</span> degenes<span class="br0">(</span>mynoiseqbio.<span class="me1">rpkm</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/q.html"><span class="kw2">q</span></a> <span class="sy0">=</span> pvtnsb, M <span class="sy0">=</span> <span class="st0">"up"</span><span class="br0">)</span>
+ mynoiseqbio.<span class="me1">rpkm</span>.<span class="me1">deg</span>.<span class="me1">down</span> <span class="sy0"><-</span> degenes<span class="br0">(</span>mynoiseqbio.<span class="me1">rpkm</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/q.html"><span class="kw2">q</span></a> <span class="sy0">=</span> pvtnsb, M <span class="sy0">=</span> <span class="st0">"down"</span><span class="br0">)</span>
+ mynoiseqbio.<span class="me1">nnorm</span>.<span class="me1">deg</span> <span class="sy0"><-</span> degenes<span class="br0">(</span>mynoiseqbio.<span class="me1">nnorm</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/q.html"><span class="kw2">q</span></a> <span class="sy0">=</span> pvtnsb, M <span class="sy0">=</span> NULL<span class="br0">)</span>
+ mynoiseqbio.<span class="me1">nnorm</span>.<span class="me1">deg</span>.<span class="me1">up</span> <span class="sy0"><-</span> degenes<span class="br0">(</span>mynoiseqbio.<span class="me1">nnorm</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/q.html"><span class="kw2">q</span></a> <span class="sy0">=</span> pvtnsb, M <span class="sy0">=</span> <span class="st0">"up"</span><span class="br0">)</span>
+ mynoiseqbio.<span class="me1">nnorm</span>.<span class="me1">deg</span>.<span class="me1">down</span> <span class="sy0"><-</span> degenes<span class="br0">(</span>mynoiseqbio.<span class="me1">nnorm</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/q.html"><span class="kw2">q</span></a> <span class="sy0">=</span> pvtnsb, M <span class="sy0">=</span> <span class="st0">"down"</span><span class="br0">)</span>
+
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/graphics/html/par.html"><span class="kw4">par</span></a><span class="br0">(</span>mfrow <span class="sy0">=</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span><span class="nu0">3</span>, <span class="nu0">2</span><span class="br0">)</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/png.html"><span class="kw5">png</span></a><span class="br0">(</span>filename<span class="sy0">=</span>paste0<span class="br0">(</span>outdir,<span class="st0">"plots/"</span>,paste0<span class="br0">(</span>cName, <span class="st0">" NOISeq - DE.rpkm_0.9"</span><span class="br0">)</span><span class="br0">)</span><span class="br0">)</span>
+ DE.<span class="me1">plot</span><span class="br0">(</span>mynoiseq.<span class="me1">rpkm</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/q.html"><span class="kw2">q</span></a> <span class="sy0">=</span> <span class="nu0">0.9</span>, graphic <span class="sy0">=</span> <span class="st0">"expr"</span>, log.<span class="me1">scale</span> <span class="sy0">=</span> TRUE<span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/dev.off.html"><span class="kw5">dev.<span class="me1">off</span></span></a><span class="br0">(</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/png.html"><span class="kw5">png</span></a><span class="br0">(</span>filename<span class="sy0">=</span>paste0<span class="br0">(</span>outdir,<span class="st0">"plots/"</span>,paste0<span class="br0">(</span>cName, <span class="st0">" NOISeq - DE.rpkm_0.8"</span><span class="br0">)</span><span class="br0">)</span><span class="br0">)</span>
+ DE.<span class="me1">plot</span><span class="br0">(</span>mynoiseq.<span class="me1">rpkm</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/q.html"><span class="kw2">q</span></a> <span class="sy0">=</span> <span class="nu0">0.8</span>, graphic <span class="sy0">=</span> <span class="st0">"expr"</span>, log.<span class="me1">scale</span> <span class="sy0">=</span> TRUE<span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/dev.off.html"><span class="kw5">dev.<span class="me1">off</span></span></a><span class="br0">(</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/png.html"><span class="kw5">png</span></a><span class="br0">(</span>filename<span class="sy0">=</span>paste0<span class="br0">(</span>outdir,<span class="st0">"plots/"</span>,paste0<span class="br0">(</span>cName, <span class="st0">" NOISeq - DE.nnorn_0.9"</span><span class="br0">)</span><span class="br0">)</span><span class="br0">)</span>
+ DE.<span class="me1">plot</span><span class="br0">(</span>mynoiseq.<span class="me1">nnorm</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/q.html"><span class="kw2">q</span></a> <span class="sy0">=</span> <span class="nu0">0.9</span>, graphic <span class="sy0">=</span> <span class="st0">"expr"</span>, log.<span class="me1">scale</span> <span class="sy0">=</span> TRUE<span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/dev.off.html"><span class="kw5">dev.<span class="me1">off</span></span></a><span class="br0">(</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/png.html"><span class="kw5">png</span></a><span class="br0">(</span>filename<span class="sy0">=</span>paste0<span class="br0">(</span>outdir,<span class="st0">"plots/"</span>,paste0<span class="br0">(</span>cName, <span class="st0">" NOISeq - DE.nnorn_0.8"</span><span class="br0">)</span><span class="br0">)</span><span class="br0">)</span>
+ DE.<span class="me1">plot</span><span class="br0">(</span>mynoiseq.<span class="me1">nnorm</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/q.html"><span class="kw2">q</span></a> <span class="sy0">=</span> <span class="nu0">0.8</span>, graphic <span class="sy0">=</span> <span class="st0">"expr"</span>, log.<span class="me1">scale</span> <span class="sy0">=</span> TRUE<span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/dev.off.html"><span class="kw5">dev.<span class="me1">off</span></span></a><span class="br0">(</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/png.html"><span class="kw5">png</span></a><span class="br0">(</span>filename<span class="sy0">=</span>paste0<span class="br0">(</span>outdir,<span class="st0">"plots/"</span>,paste0<span class="br0">(</span>cName, <span class="st0">" NOISeq - DE.tmm_0.9"</span><span class="br0">)</span><span class="br0">)</span><span class="br0">)</span>
+ DE.<span class="me1">plot</span><span class="br0">(</span>mynoiseq.<span class="me1">tmm</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/q.html"><span class="kw2">q</span></a> <span class="sy0">=</span> <span class="nu0">0.9</span>, graphic <span class="sy0">=</span> <span class="st0">"expr"</span>, log.<span class="me1">scale</span> <span class="sy0">=</span> TRUE<span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/dev.off.html"><span class="kw5">dev.<span class="me1">off</span></span></a><span class="br0">(</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/png.html"><span class="kw5">png</span></a><span class="br0">(</span>filename<span class="sy0">=</span>paste0<span class="br0">(</span>outdir,<span class="st0">"plots/"</span>,paste0<span class="br0">(</span>cName, <span class="st0">" NOISeq - DE.tmm_0.8"</span><span class="br0">)</span><span class="br0">)</span><span class="br0">)</span>
+ DE.<span class="me1">plot</span><span class="br0">(</span>mynoiseq.<span class="me1">tmm</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/q.html"><span class="kw2">q</span></a> <span class="sy0">=</span> <span class="nu0">0.8</span>, graphic <span class="sy0">=</span> <span class="st0">"expr"</span>, log.<span class="me1">scale</span> <span class="sy0">=</span> TRUE<span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/dev.off.html"><span class="kw5">dev.<span class="me1">off</span></span></a><span class="br0">(</span><span class="br0">)</span>
+
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/graphics/html/par.html"><span class="kw4">par</span></a><span class="br0">(</span>mfrow <span class="sy0">=</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span><span class="nu0">2</span>, <span class="nu0">2</span><span class="br0">)</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/png.html"><span class="kw5">png</span></a><span class="br0">(</span>filename<span class="sy0">=</span>paste0<span class="br0">(</span>outdir,<span class="st0">"plots/"</span>,paste0<span class="br0">(</span>cName, <span class="st0">" NOISeqbio - DE.rpkm_"</span>,pvt<span class="br0">)</span><span class="br0">)</span><span class="br0">)</span>
+ DE.<span class="me1">plot</span><span class="br0">(</span>mynoiseqbio.<span class="me1">rpkm</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/q.html"><span class="kw2">q</span></a> <span class="sy0">=</span> pvt, graphic <span class="sy0">=</span> <span class="st0">"expr"</span>, log.<span class="me1">scale</span> <span class="sy0">=</span> TRUE<span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/dev.off.html"><span class="kw5">dev.<span class="me1">off</span></span></a><span class="br0">(</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/png.html"><span class="kw5">png</span></a><span class="br0">(</span>filename<span class="sy0">=</span>paste0<span class="br0">(</span>outdir,<span class="st0">"plots/"</span>,paste0<span class="br0">(</span>cName, <span class="st0">" NOISeqbio - DE.rpkm_"</span>,pvtnsb<span class="br0">)</span><span class="br0">)</span><span class="br0">)</span>
+ DE.<span class="me1">plot</span><span class="br0">(</span>mynoiseqbio.<span class="me1">rpkm</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/q.html"><span class="kw2">q</span></a> <span class="sy0">=</span> pvtnsb, graphic <span class="sy0">=</span> <span class="st0">"expr"</span>, log.<span class="me1">scale</span> <span class="sy0">=</span> TRUE<span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/dev.off.html"><span class="kw5">dev.<span class="me1">off</span></span></a><span class="br0">(</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/png.html"><span class="kw5">png</span></a><span class="br0">(</span>filename<span class="sy0">=</span>paste0<span class="br0">(</span>outdir,<span class="st0">"plots/"</span>,paste0<span class="br0">(</span>cName, <span class="st0">" NOISeqbio - DE.nnorm_"</span>,pvt<span class="br0">)</span><span class="br0">)</span><span class="br0">)</span>
+ DE.<span class="me1">plot</span><span class="br0">(</span>mynoiseqbio.<span class="me1">nnorm</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/q.html"><span class="kw2">q</span></a> <span class="sy0">=</span> pvt, graphic <span class="sy0">=</span> <span class="st0">"expr"</span>, log.<span class="me1">scale</span> <span class="sy0">=</span> TRUE<span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/dev.off.html"><span class="kw5">dev.<span class="me1">off</span></span></a><span class="br0">(</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/png.html"><span class="kw5">png</span></a><span class="br0">(</span>filename<span class="sy0">=</span>paste0<span class="br0">(</span>outdir,<span class="st0">"plots/"</span>,paste0<span class="br0">(</span>cName, <span class="st0">" NOISeqbio - DE.nnorm_"</span>,pvtnsb<span class="br0">)</span><span class="br0">)</span><span class="br0">)</span>
+ DE.<span class="me1">plot</span><span class="br0">(</span>mynoiseqbio.<span class="me1">nnorm</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/q.html"><span class="kw2">q</span></a> <span class="sy0">=</span> pvtnsb, graphic <span class="sy0">=</span> <span class="st0">"expr"</span>, log.<span class="me1">scale</span> <span class="sy0">=</span> TRUE<span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/dev.off.html"><span class="kw5">dev.<span class="me1">off</span></span></a><span class="br0">(</span><span class="br0">)</span>
+
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/graphics/html/par.html"><span class="kw4">par</span></a><span class="br0">(</span>mfrow <span class="sy0">=</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span><span class="nu0">1</span>, <span class="nu0">2</span><span class="br0">)</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/png.html"><span class="kw5">png</span></a><span class="br0">(</span>filename<span class="sy0">=</span>paste0<span class="br0">(</span>outdir,<span class="st0">"plots/"</span>,paste0<span class="br0">(</span>cName, <span class="st0">" NOISeq - DE.rpkm_0.9_MD"</span><span class="br0">)</span><span class="br0">)</span><span class="br0">)</span>
+ DE.<span class="me1">plot</span><span class="br0">(</span>mynoiseq.<span class="me1">rpkm</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/q.html"><span class="kw2">q</span></a> <span class="sy0">=</span> <span class="nu0">0.9</span>, graphic <span class="sy0">=</span> <span class="st0">"MD"</span>, log.<span class="me1">scale</span> <span class="sy0">=</span> TRUE<span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/dev.off.html"><span class="kw5">dev.<span class="me1">off</span></span></a><span class="br0">(</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/png.html"><span class="kw5">png</span></a><span class="br0">(</span>filename<span class="sy0">=</span>paste0<span class="br0">(</span>outdir,<span class="st0">"plots/"</span>,paste0<span class="br0">(</span>cName, <span class="st0">" NOISeq - DE.nnorm_0.9_MD"</span><span class="br0">)</span><span class="br0">)</span><span class="br0">)</span>
+ DE.<span class="me1">plot</span><span class="br0">(</span>mynoiseq.<span class="me1">nnorm</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/q.html"><span class="kw2">q</span></a> <span class="sy0">=</span> <span class="nu0">0.9</span>, graphic <span class="sy0">=</span> <span class="st0">"MD"</span>, log.<span class="me1">scale</span> <span class="sy0">=</span> TRUE<span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/dev.off.html"><span class="kw5">dev.<span class="me1">off</span></span></a><span class="br0">(</span><span class="br0">)</span>
+<span class="br0">}</span>
+
+<span class="co1">###########################################</span>
+<span class="co1">## additional function for more usability #</span>
+<span class="co1">###########################################</span>
+
+calcRPKM <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/function.html"><span class="kw2">function</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a>,n,l<span class="br0">)</span>
+<span class="br0">{</span>
+ RPKM <span class="sy0"><-</span> <span class="br0">(</span><span class="nu0">10</span><span class="sy0">^</span><span class="nu0">9</span><span class="sy0">*</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/as.numeric.html"><span class="kw2">as.<span class="me1">numeric</span></span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">)</span><span class="br0">)</span> <span class="sy0">/</span> <span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/as.numeric.html"><span class="kw2">as.<span class="me1">numeric</span></span></a><span class="br0">(</span>n<span class="br0">)</span> <span class="sy0">*</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/as.numeric.html"><span class="kw2">as.<span class="me1">numeric</span></span></a><span class="br0">(</span>l<span class="br0">)</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/return.html"><span class="kw2">return</span></a><span class="br0">(</span>RPKM<span class="br0">)</span>
+<span class="br0">}</span>
+
+RPKMMatrix <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/function.html"><span class="kw2">function</span></a><span class="br0">(</span>InTable,directory,LenGCTable,myLenPos<span class="br0">)</span>
+<span class="br0">{</span>
+ myLengthTable <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/read.table.html"><span class="kw8">read.<span class="me1">table</span></span></a><span class="br0">(</span>paste0<span class="br0">(</span>directory,LenGCTable<span class="br0">)</span>, sep <span class="sy0">=</span> <span class="st0">"<span class="es0">\t</span>"</span>, header <span class="sy0">=</span> TRUE, stringsAsFactor <span class="sy0">=</span> FALSE, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/row.names.html"><span class="kw2">row.<span class="me1">names</span></span></a> <span class="sy0">=</span> <span class="nu0">1</span><span class="br0">)</span>
+
+ newtable <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/matrix.html"><span class="kw2">matrix</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/data.html"><span class="kw8">data</span></a> <span class="sy0">=</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span><span class="nu0">1</span><span class="br0">)</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/nrow.html"><span class="kw2">nrow</span></a> <span class="sy0">=</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/nrow.html"><span class="kw2">nrow</span></a><span class="br0">(</span>InTable<span class="br0">)</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/ncol.html"><span class="kw2">ncol</span></a><span class="br0">(</span>InTable<span class="br0">)</span>, byrow<span class="sy0">=</span> TRUE<span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/colnames.html"><span class="kw2">colnames</span></a><span class="br0">(</span>newtable<span class="br0">)</span> <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/colnames.html"><span class="kw2">colnames</span></a><span class="br0">(</span>InTable<span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/rownames.html"><span class="kw2">rownames</span></a><span class="br0">(</span>newtable<span class="br0">)</span> <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/rownames.html"><span class="kw2">rownames</span></a><span class="br0">(</span>InTable<span class="br0">)</span>
+
+ sumCol <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/apply.html"><span class="kw2">apply</span></a><span class="br0">(</span>InTable,<span class="nu0">2</span>,<a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/sum.html"><span class="kw2">sum</span></a><span class="br0">)</span> <span class="co1"># list of the all col sums</span>
+
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/for.html"><span class="kw2">for</span></a><span class="br0">(</span>s <span class="kw1">in</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/colnames.html"><span class="kw2">colnames</span></a><span class="br0">(</span>InTable<span class="br0">)</span><span class="br0">)</span> <span class="br0">{</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/for.html"><span class="kw2">for</span></a><span class="br0">(</span>r <span class="kw1">in</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/rownames.html"><span class="kw2">rownames</span></a><span class="br0">(</span>InTable<span class="br0">)</span><span class="br0">)</span> <span class="br0">{</span>
+ w <span class="sy0"><-</span> InTable<span class="br0">[</span>r, s<span class="br0">]</span>
+ len <span class="sy0"><-</span> myLengthTable<span class="br0">[</span>r, myLenPos<span class="br0">]</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/sum.html"><span class="kw2">sum</span></a> <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/as.numeric.html"><span class="kw2">as.<span class="me1">numeric</span></span></a><span class="br0">(</span>sumCol<span class="br0">[</span>s<span class="br0">]</span><span class="br0">)</span>
+
+ newtable<span class="br0">[</span>r, s<span class="br0">]</span> <span class="sy0"><-</span> calcRPKM<span class="br0">(</span>w, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/sum.html"><span class="kw2">sum</span></a>, len<span class="br0">)</span>
+ <span class="br0">}</span>
+ <span class="br0">}</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/return.html"><span class="kw2">return</span></a><span class="br0">(</span>newtable<span class="br0">)</span>
+<span class="br0">}</span>
+
+
+<span class="co1"># rmHTSeqLines removes the last five rows</span>
+rmHTSeqLines <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/function.html"><span class="kw2">function</span></a><span class="br0">(</span>counts<span class="br0">)</span>
+<span class="br0">{</span>
+ counts <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/head.html"><span class="kw8">head</span></a><span class="br0">(</span>counts, <span class="sy0">-</span><span class="nu0">5</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/return.html"><span class="kw2">return</span></a><span class="br0">(</span>counts<span class="br0">)</span>
+<span class="br0">}</span>
+
+
+<span class="co1">###############</span>
+<span class="co1">## functions ##</span>
+<span class="co1">###############</span>
+
+<span class="co1"># split list to a factor list</span>
+split2list <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/function.html"><span class="kw2">function</span></a><span class="br0">(</span>tmp<span class="br0">)</span>
+<span class="br0">{</span>
+ xx <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/for.html"><span class="kw2">for</span></a><span class="br0">(</span>i <span class="kw1">in</span> <span class="nu0">1</span><span class="sy0">:</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/length.html"><span class="kw2">length</span></a><span class="br0">(</span>tmp<span class="br0">)</span><span class="br0">)</span> <span class="br0">{</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/if.html"><span class="kw2">if</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/grepl.html"><span class="kw2">grepl</span></a><span class="br0">(</span><span class="st0">"<span class="es0">\\</span>."</span>, tmp<span class="br0">[</span>i<span class="br0">]</span><span class="br0">)</span><span class="br0">)</span> <span class="br0">{</span>
+ foo <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/strsplit.html"><span class="kw2">strsplit</span></a><span class="br0">(</span>tmp<span class="br0">[</span>i<span class="br0">]</span>, <span class="st0">'<span class="es0">\\</span>.'</span><span class="br0">)</span><span class="br0">[</span><span class="br0">[</span><span class="nu0">1</span><span class="br0">]</span><span class="br0">]</span>
+ fooo <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/strsplit.html"><span class="kw2">strsplit</span></a><span class="br0">(</span>foo, <span class="st0">" "</span><span class="br0">)</span><span class="br0">[</span><span class="br0">[</span><span class="nu0">1</span><span class="br0">]</span><span class="br0">]</span>
+ xx <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span>xx, fooo<span class="br0">)</span>
+ <span class="br0">}</span> <span class="kw1">else</span> <span class="br0">{</span>
+ xx <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span>xx, tmp<span class="br0">[</span>i<span class="br0">]</span><span class="br0">)</span>
+ <span class="br0">}</span>
+ <span class="br0">}</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/return.html"><span class="kw2">return</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/as.factor.html"><span class="kw2">as.<span class="me1">factor</span></span></a><span class="br0">(</span>xx<span class="br0">)</span><span class="br0">)</span>
+<span class="br0">}</span>
+
+<span class="co1"># makeGroups</span>
+<span class="co1"># https://github.com/drisso/RUVSeq/blob/master/R/helper.R</span>
+makeGroups <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/function.html"><span class="kw2">function</span></a><span class="br0">(</span>xs<span class="br0">)</span>
+<span class="br0">{</span>
+ xs <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/factor.html"><span class="kw2">factor</span></a><span class="br0">(</span>xs<span class="br0">)</span>
+ groups <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/matrix.html"><span class="kw2">matrix</span></a><span class="br0">(</span><span class="sy0">-</span><span class="nu0">1</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/nrow.html"><span class="kw2">nrow</span></a> <span class="sy0">=</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/length.html"><span class="kw2">length</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/levels.html"><span class="kw2">levels</span></a><span class="br0">(</span>xs<span class="br0">)</span><span class="br0">)</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/ncol.html"><span class="kw2">ncol</span></a> <span class="sy0">=</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/max.html"><span class="kw2">max</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/table.html"><span class="kw2">table</span></a><span class="br0">(</span>xs<span class="br0">)</span><span class="br0">)</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/for.html"><span class="kw2">for</span></a> <span class="br0">(</span>i <span class="kw1">in</span> <span class="nu0">1</span><span class="sy0">:</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/length.html"><span class="kw2">length</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/levels.html"><span class="kw2">levels</span></a><span class="br0">(</span>xs<span class="br0">)</span><span class="br0">)</span><span class="br0">)</span> <span class="br0">{</span>
+ idxs <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/which.html"><span class="kw2">which</span></a><span class="br0">(</span>xs <span class="sy0">==</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/levels.html"><span class="kw2">levels</span></a><span class="br0">(</span>xs<span class="br0">)</span><span class="br0">[</span>i<span class="br0">]</span><span class="br0">)</span>
+ groups<span class="br0">[</span>i,<span class="nu0">1</span><span class="sy0">:</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/length.html"><span class="kw2">length</span></a><span class="br0">(</span>idxs<span class="br0">)</span><span class="br0">]</span> <span class="sy0"><-</span> idxs
+ <span class="br0">}</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/return.html"><span class="kw2">return</span></a><span class="br0">(</span>groups<span class="br0">)</span>
+<span class="br0">}</span>
+
+<span class="co1"># The function makeSampleList creates a list of the columns(samples) you would like to compare</span>
+makeSampleList <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/function.html"><span class="kw2">function</span></a><span class="br0">(</span>A, Al, B, Bl<span class="br0">)</span>
+<span class="br0">{</span>
+ l <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/if.html"><span class="kw2">if</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/exists.html"><span class="kw2">exists</span></a><span class="br0">(</span><span class="st0">"Al"</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/mode.html"><span class="kw2">mode</span></a> <span class="sy0">=</span> <span class="st0">"numeric"</span><span class="br0">)</span><span class="br0">)</span> <span class="br0">{</span>
+ l <span class="sy0"><-</span> makeSampleList.<span class="me1">helper</span><span class="br0">(</span>A, Al, l<span class="br0">)</span>
+ l <span class="sy0"><-</span> makeSampleList.<span class="me1">helper</span><span class="br0">(</span>B, Bl, l<span class="br0">)</span>
+ <span class="br0">}</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/return.html"><span class="kw2">return</span></a><span class="br0">(</span>l<span class="br0">)</span>
+<span class="br0">}</span>
+makeSampleList.<span class="me1">helper</span> <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/function.html"><span class="kw2">function</span></a><span class="br0">(</span>v,k,l<span class="br0">)</span>
+<span class="br0">{</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/for.html"><span class="kw2">for</span></a><span class="br0">(</span>h <span class="kw1">in</span> <span class="nu0">1</span><span class="sy0">:</span>k<span class="br0">)</span> <span class="br0">{</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/if.html"><span class="kw2">if</span></a><span class="br0">(</span>h <span class="sy0">==</span> <span class="nu0">1</span><span class="br0">)</span> <span class="br0">{</span>
+ l <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span>l, v<span class="br0">)</span>
+ <span class="br0">}</span> <span class="kw1">else</span> <span class="br0">{</span>
+ l <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span>l, paste0<span class="br0">(</span>v,<span class="st0">"."</span>,h<span class="sy0">-</span><span class="nu0">1</span><span class="br0">)</span><span class="br0">)</span>
+ <span class="br0">}</span>
+ <span class="br0">}</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/return.html"><span class="kw2">return</span></a><span class="br0">(</span>l<span class="br0">)</span>
+<span class="br0">}</span>
+
+<span class="co1"># function creates a list of numbers out of another list. The List is the index of the given list.</span>
+makeIndexList <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/function.html"><span class="kw2">function</span></a><span class="br0">(</span>l<span class="br0">)</span>
+<span class="br0">{</span>
+ n <span class="sy0"><-</span> <span class="nu0">1</span>
+ jj <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/for.html"><span class="kw2">for</span></a><span class="br0">(</span>v <span class="kw1">in</span> l<span class="br0">)</span> <span class="br0">{</span>
+ jj <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span>jj, n<span class="br0">)</span>
+ n <span class="sy0"><-</span> n <span class="sy0">+</span> <span class="nu0">1</span>
+ <span class="br0">}</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/return.html"><span class="kw2">return</span></a><span class="br0">(</span>jj<span class="br0">)</span>
+<span class="br0">}</span>
+
+intersection <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/function.html"><span class="kw2">function</span></a><span class="br0">(</span>l,check,<a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/t.html"><span class="kw2">t</span></a><span class="br0">)</span>
+<span class="br0">{</span>
+ l.<span class="me1">list</span> <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/list.files.html"><span class="kw2">list.<span class="me1">files</span></span></a><span class="br0">(</span>path <span class="sy0">=</span> l, pattern <span class="sy0">=</span> <span class="st0">"*(rpkm|edgeR|DESeq2).*tsv"</span>, recursive <span class="sy0">=</span> TRUE<span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/if.html"><span class="kw2">if</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/grepl.html"><span class="kw2">grepl</span></a><span class="br0">(</span><span class="st0">"bio"</span>, l.<span class="me1">list</span><span class="br0">[</span><span class="nu0">4</span><span class="br0">]</span>,fixed <span class="sy0">=</span> TRUE<span class="br0">)</span><span class="br0">)</span> <span class="br0">{</span>
+ l.<span class="me1">list</span>.<span class="me1">noiseq</span> <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/read.table.html"><span class="kw8">read.<span class="me1">table</span></span></a><span class="br0">(</span>paste0<span class="br0">(</span>l,<span class="st0">"/"</span>,l.<span class="me1">list</span><span class="br0">[</span><span class="nu0">3</span><span class="br0">]</span><span class="br0">)</span>, header<span class="sy0">=</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/T.html"><span class="kw2">T</span></a>, sep<span class="sy0">=</span><span class="st0">"<span class="es0">\t</span>"</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/row.names.html"><span class="kw2">row.<span class="me1">names</span></span></a><span class="sy0">=</span><span class="nu0">1</span><span class="br0">)</span>
+ l.<span class="me1">list</span>.<span class="me1">noiseqbio</span> <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/read.table.html"><span class="kw8">read.<span class="me1">table</span></span></a><span class="br0">(</span>paste0<span class="br0">(</span>l,<span class="st0">"/"</span>,l.<span class="me1">list</span><span class="br0">[</span><span class="nu0">4</span><span class="br0">]</span><span class="br0">)</span>, header<span class="sy0">=</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/T.html"><span class="kw2">T</span></a>, sep<span class="sy0">=</span><span class="st0">"<span class="es0">\t</span>"</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/row.names.html"><span class="kw2">row.<span class="me1">names</span></span></a><span class="sy0">=</span><span class="nu0">1</span><span class="br0">)</span>
+ <span class="br0">}</span> <span class="kw1">else</span> <span class="br0">{</span>
+ l.<span class="me1">list</span>.<span class="me1">noiseq</span> <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/read.table.html"><span class="kw8">read.<span class="me1">table</span></span></a><span class="br0">(</span>paste0<span class="br0">(</span>l,<span class="st0">"/"</span>,l.<span class="me1">list</span><span class="br0">[</span><span class="nu0">4</span><span class="br0">]</span><span class="br0">)</span>, header<span class="sy0">=</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/T.html"><span class="kw2">T</span></a>, sep<span class="sy0">=</span><span class="st0">"<span class="es0">\t</span>"</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/row.names.html"><span class="kw2">row.<span class="me1">names</span></span></a><span class="sy0">=</span><span class="nu0">1</span><span class="br0">)</span>
+ l.<span class="me1">list</span>.<span class="me1">noiseqbio</span> <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/read.table.html"><span class="kw8">read.<span class="me1">table</span></span></a><span class="br0">(</span>paste0<span class="br0">(</span>l,<span class="st0">"/"</span>,l.<span class="me1">list</span><span class="br0">[</span><span class="nu0">3</span><span class="br0">]</span><span class="br0">)</span>, header<span class="sy0">=</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/T.html"><span class="kw2">T</span></a>, sep<span class="sy0">=</span><span class="st0">"<span class="es0">\t</span>"</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/row.names.html"><span class="kw2">row.<span class="me1">names</span></span></a><span class="sy0">=</span><span class="nu0">1</span><span class="br0">)</span>
+ <span class="br0">}</span>
+ l.<span class="me1">list</span>.<span class="me1">edgeR</span> <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/read.table.html"><span class="kw8">read.<span class="me1">table</span></span></a><span class="br0">(</span>paste0<span class="br0">(</span>l,<span class="st0">"/"</span>,l.<span class="me1">list</span><span class="br0">[</span><span class="nu0">2</span><span class="br0">]</span><span class="br0">)</span>, header<span class="sy0">=</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/T.html"><span class="kw2">T</span></a>, sep<span class="sy0">=</span><span class="st0">"<span class="es0">\t</span>"</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/row.names.html"><span class="kw2">row.<span class="me1">names</span></span></a><span class="sy0">=</span><span class="nu0">1</span><span class="br0">)</span>
+ l.<span class="me1">list</span>.<span class="me1">deseq2</span> <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/read.table.html"><span class="kw8">read.<span class="me1">table</span></span></a><span class="br0">(</span>paste0<span class="br0">(</span>l,<span class="st0">"/"</span>,l.<span class="me1">list</span><span class="br0">[</span><span class="nu0">1</span><span class="br0">]</span><span class="br0">)</span>, header<span class="sy0">=</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/T.html"><span class="kw2">T</span></a>, sep<span class="sy0">=</span><span class="st0">"<span class="es0">\t</span>"</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/row.names.html"><span class="kw2">row.<span class="me1">names</span></span></a><span class="sy0">=</span><span class="nu0">1</span><span class="br0">)</span>
+
+
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span><span class="st0">"DEGs edgeR"</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/nrow.html"><span class="kw2">nrow</span></a><span class="br0">(</span>l.<span class="me1">list</span>.<span class="me1">edgeR</span><span class="br0">)</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span><span class="st0">"DEGs deseq2"</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/nrow.html"><span class="kw2">nrow</span></a><span class="br0">(</span>l.<span class="me1">list</span>.<span class="me1">deseq2</span><span class="br0">)</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span><span class="st0">"DEGs noiseq"</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/nrow.html"><span class="kw2">nrow</span></a><span class="br0">(</span>l.<span class="me1">list</span>.<span class="me1">noiseq</span><span class="br0">)</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span><span class="st0">"DEGs noiseqbio"</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/nrow.html"><span class="kw2">nrow</span></a><span class="br0">(</span>l.<span class="me1">list</span>.<span class="me1">noiseqbio</span><span class="br0">)</span><span class="br0">)</span>
+
+ interect.<span class="me1">list</span> <span class="sy0"><-</span> <span class="st0">""</span>
+ interect.<span class="me1">list</span>.<span class="me1">direct</span> <span class="sy0"><-</span> <span class="st0">""</span>
+
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/if.html"><span class="kw2">if</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/t.html"><span class="kw2">t</span></a><span class="sy0">==</span><span class="nu0">4</span><span class="br0">)</span> <span class="br0">{</span>
+ <span class="co1"># List of overlaps without direction check</span>
+ interect.<span class="me1">list</span> <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/intersect.html"><span class="kw2">intersect</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/rownames.html"><span class="kw2">rownames</span></a><span class="br0">(</span>l.<span class="me1">list</span>.<span class="me1">edgeR</span><span class="br0">)</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/intersect.html"><span class="kw2">intersect</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/rownames.html"><span class="kw2">rownames</span></a><span class="br0">(</span>l.<span class="me1">list</span>.<span class="me1">noiseq</span><span class="br0">)</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/intersect.html"><span class="kw2">intersect</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/rownames.html"><span class="kw2">rownames</span></a><span class="br0">(</span>l.<span class="me1">list</span>.<span class="me1">noiseqbio</span><span class="br0">)</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/rownames.html"><span class="kw2">rownames</span></a><span class="br0">(</span>l.<span class="me1">list</span>.<span class="me1">deseq2</span><span class="br0">)</span><span class="br0">)</span><span class="br0">)</span><span class="br0">)</span>
+
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span><span class="st0">"DEGs intersection without direction check (four methods)"</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/length.html"><span class="kw2">length</span></a><span class="br0">(</span>interect.<span class="me1">list</span><span class="br0">)</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span>interect.<span class="me1">list</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span><span class="st0">"DEGs intersection with direction check"</span><span class="br0">)</span>
+
+ <span class="co1"># List of overlaps with direction check</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/if.html"><span class="kw2">if</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/length.html"><span class="kw2">length</span></a><span class="br0">(</span>interect.<span class="me1">list</span><span class="br0">)</span><span class="sy0">!=</span><span class="nu0">0</span><span class="br0">)</span> <span class="br0">{</span>
+ interect.<span class="me1">list</span>.<span class="me1">direct</span> <span class="sy0"><-</span> interDirect<span class="br0">(</span>l.<span class="me1">list</span>.<span class="me1">edgeR</span>, l.<span class="me1">list</span>.<span class="me1">deseq2</span>, l.<span class="me1">list</span>.<span class="me1">noiseq</span>, l.<span class="me1">list</span>.<span class="me1">noiseqbio</span>, interect.<span class="me1">list</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/length.html"><span class="kw2">length</span></a><span class="br0">(</span>interect.<span class="me1">list</span>.<span class="me1">direct</span><span class="br0">)</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span>interect.<span class="me1">list</span>.<span class="me1">direct</span><span class="br0">)</span>
+ <span class="br0">}</span> <span class="kw1">else</span> <span class="br0">{</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span><span class="st0">"0"</span><span class="br0">)</span>
+ <span class="br0">}</span>
+ <span class="br0">}</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/if.html"><span class="kw2">if</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/t.html"><span class="kw2">t</span></a><span class="sy0">==</span><span class="nu0">3</span><span class="br0">)</span> <span class="br0">{</span>
+ <span class="co1"># List of overlaps without direction check</span>
+ interect.<span class="me1">list</span> <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/intersect.html"><span class="kw2">intersect</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/rownames.html"><span class="kw2">rownames</span></a><span class="br0">(</span>l.<span class="me1">list</span>.<span class="me1">edgeR</span><span class="br0">)</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/intersect.html"><span class="kw2">intersect</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/rownames.html"><span class="kw2">rownames</span></a><span class="br0">(</span>l.<span class="me1">list</span>.<span class="me1">noiseq</span><span class="br0">)</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/rownames.html"><span class="kw2">rownames</span></a><span class="br0">(</span>l.<span class="me1">list</span>.<span class="me1">deseq2</span><span class="br0">)</span><span class="br0">)</span><span class="br0">)</span>
+
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span><span class="st0">"DEGs intersection without direction check (three methods)"</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/length.html"><span class="kw2">length</span></a><span class="br0">(</span>interect.<span class="me1">list</span><span class="br0">)</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span>interect.<span class="me1">list</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span><span class="st0">"DEGs intersection with direction check"</span><span class="br0">)</span>
+
+ <span class="co1"># List of overlaps with direction check</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/if.html"><span class="kw2">if</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/length.html"><span class="kw2">length</span></a><span class="br0">(</span>interect.<span class="me1">list</span><span class="br0">)</span><span class="sy0">!=</span><span class="nu0">0</span><span class="br0">)</span> <span class="br0">{</span>
+ <span class="co1"># fake data frame with 0 rows => nrow == 0</span>
+ df_fake <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/data.frame.html"><span class="kw2">data.<span class="me1">frame</span></span></a><span class="br0">(</span>Date<span class="sy0">=</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/as.Date.html"><span class="kw2">as.<span class="me1">Date</span></span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/character.html"><span class="kw2">character</span></a><span class="br0">(</span><span class="br0">)</span><span class="br0">)</span>,
+ File<span class="sy0">=</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/character.html"><span class="kw2">character</span></a><span class="br0">(</span><span class="br0">)</span>,
+ User<span class="sy0">=</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/character.html"><span class="kw2">character</span></a><span class="br0">(</span><span class="br0">)</span>,
+ stringsAsFactors<span class="sy0">=</span>FALSE<span class="br0">)</span>
+
+ interect.<span class="me1">list</span>.<span class="me1">direct</span> <span class="sy0"><-</span> interDirect<span class="br0">(</span>l.<span class="me1">list</span>.<span class="me1">edgeR</span>, l.<span class="me1">list</span>.<span class="me1">deseq2</span>, l.<span class="me1">list</span>.<span class="me1">noiseq</span>, df_fake, interect.<span class="me1">list</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/length.html"><span class="kw2">length</span></a><span class="br0">(</span>interect.<span class="me1">list</span>.<span class="me1">direct</span><span class="br0">)</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span>interect.<span class="me1">list</span>.<span class="me1">direct</span><span class="br0">)</span>
+ <span class="br0">}</span> <span class="kw1">else</span> <span class="br0">{</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span><span class="st0">"0"</span><span class="br0">)</span>
+ <span class="br0">}</span>
+ <span class="br0">}</span>
+
+
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/if.html"><span class="kw2">if</span></a><span class="br0">(</span>check <span class="sy0">==</span> <span class="nu0">1</span><span class="br0">)</span><span class="br0">{</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/return.html"><span class="kw2">return</span></a><span class="br0">(</span>l.<span class="me1">list</span>.<span class="me1">noiseq</span><span class="br0">[</span>interect.<span class="me1">list</span>.<span class="me1">direct</span>,<span class="br0">]</span><span class="br0">)</span>
+ <span class="br0">}</span> <span class="kw1">else</span> <span class="br0">{</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/return.html"><span class="kw2">return</span></a><span class="br0">(</span>l.<span class="me1">list</span>.<span class="me1">noiseq</span><span class="br0">[</span>interect.<span class="me1">list</span>,<span class="br0">]</span><span class="br0">)</span>
+ <span class="br0">}</span>
+<span class="br0">}</span>
+
+interDirect <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/function.html"><span class="kw2">function</span></a><span class="br0">(</span>e,d,n,nb,i<span class="br0">)</span>
+<span class="br0">{</span>
+
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/if.html"><span class="kw2">if</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/nrow.html"><span class="kw2">nrow</span></a><span class="br0">(</span>nb<span class="br0">)</span> <span class="sy0">==</span> <span class="nu0">0</span><span class="br0">)</span> <span class="br0">{</span>
+ nbx <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/apply.html"><span class="kw2">apply</span></a><span class="br0">(</span>n<span class="br0">[</span>i,<span class="br0">]</span>, <span class="nu0">2</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/function.html"><span class="kw2">function</span></a><span class="br0">(</span>x<span class="br0">)</span> <span class="br0">{</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/ifelse.html"><span class="kw2">ifelse</span></a><span class="br0">(</span>x <span class="sy0">></span> <span class="nu0">0</span>, <span class="st0">"-"</span>, <span class="st0">"+"</span><span class="br0">)</span><span class="br0">}</span><span class="br0">)</span> <span class="co1"># use noiseq twice to simulate noiseqbio</span>
+ nby <span class="sy0"><-</span> paste0<span class="br0">(</span>nbx<span class="br0">[</span>,<span class="st0">"M"</span><span class="br0">]</span>,<a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/rownames.html"><span class="kw2">rownames</span></a><span class="br0">(</span>nbx<span class="br0">)</span><span class="br0">)</span>
+ <span class="br0">}</span> <span class="kw1">else</span> <span class="br0">{</span>
+ nbx <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/apply.html"><span class="kw2">apply</span></a><span class="br0">(</span>nb<span class="br0">[</span>i,<span class="br0">]</span>, <span class="nu0">2</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/function.html"><span class="kw2">function</span></a><span class="br0">(</span>x<span class="br0">)</span> <span class="br0">{</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/ifelse.html"><span class="kw2">ifelse</span></a><span class="br0">(</span>x <span class="sy0">></span> <span class="nu0">0</span>, <span class="st0">"-"</span>, <span class="st0">"+"</span><span class="br0">)</span><span class="br0">}</span><span class="br0">)</span>
+ nby <span class="sy0"><-</span> paste0<span class="br0">(</span>nbx<span class="br0">[</span>,<span class="st0">"log2FC"</span><span class="br0">]</span>,<a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/rownames.html"><span class="kw2">rownames</span></a><span class="br0">(</span>nbx<span class="br0">)</span><span class="br0">)</span>
+ <span class="br0">}</span>
+
+ ex <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/apply.html"><span class="kw2">apply</span></a><span class="br0">(</span>e<span class="br0">[</span>i,<span class="br0">]</span>, <span class="nu0">2</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/function.html"><span class="kw2">function</span></a><span class="br0">(</span>x<span class="br0">)</span> <span class="br0">{</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/ifelse.html"><span class="kw2">ifelse</span></a><span class="br0">(</span>x <span class="sy0"><</span> <span class="nu0">0</span>, <span class="st0">"-"</span>, <span class="st0">"+"</span><span class="br0">)</span><span class="br0">}</span><span class="br0">)</span>
+ dx <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/apply.html"><span class="kw2">apply</span></a><span class="br0">(</span>d<span class="br0">[</span>i,<span class="br0">]</span>, <span class="nu0">2</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/function.html"><span class="kw2">function</span></a><span class="br0">(</span>x<span class="br0">)</span> <span class="br0">{</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/ifelse.html"><span class="kw2">ifelse</span></a><span class="br0">(</span>x <span class="sy0"><</span> <span class="nu0">0</span>, <span class="st0">"-"</span>, <span class="st0">"+"</span><span class="br0">)</span><span class="br0">}</span><span class="br0">)</span>
+ nx <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/apply.html"><span class="kw2">apply</span></a><span class="br0">(</span>n<span class="br0">[</span>i,<span class="br0">]</span>, <span class="nu0">2</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/function.html"><span class="kw2">function</span></a><span class="br0">(</span>x<span class="br0">)</span> <span class="br0">{</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/ifelse.html"><span class="kw2">ifelse</span></a><span class="br0">(</span>x <span class="sy0">></span> <span class="nu0">0</span>, <span class="st0">"-"</span>, <span class="st0">"+"</span><span class="br0">)</span><span class="br0">}</span><span class="br0">)</span> <span class="co1"># twisted, because edgeR and DESeq2 are calculating vice versa</span>
+
+ ey <span class="sy0"><-</span> paste0<span class="br0">(</span>ex<span class="br0">[</span>,<span class="st0">"logFC"</span><span class="br0">]</span>,<a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/rownames.html"><span class="kw2">rownames</span></a><span class="br0">(</span>ex<span class="br0">)</span><span class="br0">)</span>
+ dy <span class="sy0"><-</span> paste0<span class="br0">(</span>dx<span class="br0">[</span>,<span class="st0">"log2FoldChange"</span><span class="br0">]</span>,<a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/rownames.html"><span class="kw2">rownames</span></a><span class="br0">(</span>dx<span class="br0">)</span><span class="br0">)</span>
+ ny <span class="sy0"><-</span> paste0<span class="br0">(</span>nx<span class="br0">[</span>,<span class="st0">"M"</span><span class="br0">]</span>,<a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/rownames.html"><span class="kw2">rownames</span></a><span class="br0">(</span>nx<span class="br0">)</span><span class="br0">)</span>
+
+ interect.<span class="me1">list</span>.<span class="me1">direct</span> <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/intersect.html"><span class="kw2">intersect</span></a><span class="br0">(</span>ey, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/intersect.html"><span class="kw2">intersect</span></a><span class="br0">(</span>dy, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/intersect.html"><span class="kw2">intersect</span></a><span class="br0">(</span>ny, nby<span class="br0">)</span><span class="br0">)</span><span class="br0">)</span>
+
+
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/return.html"><span class="kw2">return</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/substr.html"><span class="kw2">substr</span></a><span class="br0">(</span>interect.<span class="me1">list</span>.<span class="me1">direct</span>,<span class="nu0">2</span>,<span class="nu0">100</span><span class="br0">)</span><span class="br0">)</span>
+<span class="br0">}</span>
+
+<span class="co1">###########################################</span>
+<span class="co1">## executiv part of the script #</span>
+<span class="co1">###########################################</span>
+<a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/for.html"><span class="kw2">for</span></a><span class="br0">(</span>SampleNames <span class="kw1">in</span> sampleLists<span class="br0">)</span> <span class="br0">{</span>
+ workflow<span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/file.html"><span class="kw2">file</span></a>, saveat, SampleNames, LenGCTable, myLenPos, myGCPos, rpkm, pvtedgeR, pvtDESeq2, pvtNOISeq, edgeRDir, DESeq2Dir, NOISeqDir, htseq<span class="br0">)</span>
+<span class="br0">}</span>
+<a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html"><span class="kw2">print</span></a><span class="br0">(</span><span class="st0">"Thank you for using the DEG pipeline :) <span class="es0">\n</span>"</span><span class="br0">)</span>
+
+<span class="co1"># fin</span>
+
+<span class="co1">### compare DEGs analysis ###</span>
+<span class="co1"># used venny and Excel</span></pre>
+</dd></dl>
+
+ <!-- wikipage stop -->
+ </div>
+
+ <div class="docInfo"><bdi>personal/haasf/2021/madland/new_deg_pipe_four_methods_noiseqbio_hoecker_20210527.txt</bdi> · Last modified: 2021/06/01 12:26 by <bdi>Fabian Haas</bdi></div>
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diff --git a/workflows/personal haasf 2021 madland rnaseqhoecker 3d_pca_plot_hoecker_20210527.r b/workflows/personal haasf 2021 madland rnaseqhoecker 3d_pca_plot_hoecker_20210527.r
new file mode 100644
index 0000000..a96f5e3
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+<dd><pre class="code file rsplus"><span class="co1"># 3d R plot</span>
+saveat <span class="sy0"><-</span> <span class="st0">"/mnt/NAS_coruscant_datashare/haasf/madland_RNA-seq_Hoecker"</span>
+
+file.<span class="me1">rpkm</span> <span class="sy0"><-</span> <span class="st0">'/mnt/NAS_coruscant_datashare/haasf/madland_RNA-seq_Hoecker/31315.p.sort.rpkm'</span>
+
+
+<span class="co1">## Windows ###</span>
+<span class="co1">#-#saveat <- "Q:/haasf/leubner_RNA-seq/Celery/DEGs_0.9/"</span>
+
+<span class="co1">#-#file.rpkm <- 'Q:/haasf/leubner_RNA-seq/Celery/DEGs/Celery_merged_isoforms.p.sort.rpkm'</span>
+<span class="co1">#-#file.count <- 'Q:/haasf/leubner_RNA-seq/Celery/DEGs_0.9/Celery_merged_isoforms.p.sort.counts'</span>
+<span class="co1">###</span>
+
+data.<span class="me1">rpkm</span> <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/read.table.html"><span class="kw8">read.<span class="me1">table</span></span></a><span class="br0">(</span>file.<span class="me1">rpkm</span>, header<span class="sy0">=</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/T.html"><span class="kw2">T</span></a>, sep<span class="sy0">=</span><span class="st0">"<span class="es0">\t</span>"</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/row.names.html"><span class="kw2">row.<span class="me1">names</span></span></a><span class="sy0">=</span><span class="nu0">1</span><span class="br0">)</span>
+
+
+<span class="co1"># sort by colnames</span>
+data.<span class="me1">rpkm</span> <span class="sy0"><-</span> data.<span class="me1">rpkm</span><span class="br0">[</span>,<a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/order.html"><span class="kw2">order</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/colnames.html"><span class="kw2">colnames</span></a><span class="br0">(</span>data.<span class="me1">rpkm</span><span class="br0">)</span><span class="br0">)</span><span class="br0">]</span>
+
+
+librariesName <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/list.html"><span class="kw2">list</span></a><span class="br0">(</span>
+ cop_D <span class="sy0">=</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span><span class="st0">"cop_D"</span>, <span class="st0">"red"</span><span class="br0">)</span>,
+ cop_L <span class="sy0">=</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span><span class="st0">"cop_L"</span>, <span class="st0">"blue"</span><span class="br0">)</span>,
+ spa_D <span class="sy0">=</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span><span class="st0">"spa_D"</span>, <span class="st0">"green"</span><span class="br0">)</span>,
+ spa_L <span class="sy0">=</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span><span class="st0">"spa_L"</span>, <span class="st0">"yellow"</span><span class="br0">)</span>,
+ WT_D <span class="sy0">=</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span><span class="st0">"WT_D"</span>, <span class="st0">"black"</span><span class="br0">)</span>,
+ WT_L <span class="sy0">=</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span><span class="st0">"WT_L"</span>, <span class="st0">"violet"</span><span class="br0">)</span>
+<span class="br0">)</span>
+
+<span class="co1"># </span>
+<span class="co1"># header.ori <- c("56754_WT_Naturally_3.bam.sort.fastq.unmapped.sam.sort.bam", "56753_WT_Naturally_2.bam.sort.fastq.unmapped.sam.sort.bam", "56752_WT_Naturally_1.bam.sort.fastq.unmapped.sam.sort.bam", "56751_tt_6_days_3.bam.sort.fastq.unmapped.sam.sort.bam", "56750_tt_6_days_2.bam.sort.fastq.unmapped.sam.sort.bam", "56749_tt_6_days_1.bam.sort.fastq.unmapped.sam.sort.bam", "56748_tt_0_days_3.bam.sort.fastq.unmapped.sam.sort.bam", "56747_tt_0_days_2.bam.sort.fastq.unmapped.sam.sort.bam", "56746_tt_0_days_1.bam.sort.fastq.unmapped.sam.sort.bam", "56745_WT_10_days_3.bam.sort.fastq.unmapped.sam.sort.bam", "56744_WT_10_days_2.bam.sort.fastq.unmapped.sam.sort.bam", "56743_WT_10_days_1.bam.sort.fastq.unmapped.sam.sort.bam", "56742_WT_6_days_3.bam.sort.fastq.unmapped.sam.sort.bam", "56741_WT_6_days_2.bam.sort.fastq.unmapped.sam.sort.bam", "56740_WT_6_days_1.bam.sort.fastq.unmapped.sam.sort.bam", "56739_WT_0_days_3.bam.sort.fastq.unmapped.sam.sort.bam", "56738_WT_0_days_2.bam.sort.fastq.unmapped.sam.sort.bam", "56737_WT_0_days_1.bam.sort.fastq.unmapped.sam.sort.bam", "56736_tt_T1_tt_6d_3.bam.sort.fastq.unmapped.sam.sort.bam", "56735_tt_T1_tt_6d_2.bam.sort.fastq.unmapped.sam.sort.bam", "56734_tt_T1_tt_6d_1.bam.sort.fastq.unmapped.sam.sort.bam", "56733_tt_T1_tt_0d_3.bam.sort.fastq.unmapped.sam.sort.bam", "56732_tt_T1_tt_0d_2.bam.sort.fastq.unmapped.sam.sort.bam", "56731_tt_T1_tt_0d_1.bam.sort.fastq.unmapped.sam.sort.bam", "56730_tt_T1_tt_0d_3.bam.sort.fastq.unmapped.sam.sort.bam", "56729_tt_T1_tt_0d_2.bam.sort.fastq.unmapped.sam.sort.bam", "56728_tt_T1_tt_0d_1.bam.sort.fastq.unmapped.sam.sort.bam", "56727_WT_T1_NA_3.bam.sort.fastq.unmapped.sam.sort.bam", "56726_WT_T1_NA_2.bam.sort.fastq.unmapped.sam.sort.bam", "56725_WT_T1_NA_1.bam.sort.fastq.unmapped.sam.sort.bam", "56724_WT_T1_WT_0d_3.bam.sort.fastq.unmapped.sam.sort.bam", "56723_WT_T1_WT_0d_2.bam.sort.fastq.unmapped.sam.sort.bam", "56722_WT_T1_WT_0d_1.bam.sort.fastq.unmapped.sam.sort.bam", "56721_WT_T1_WT_10d_3.bam.sort.fastq.unmapped.sam.sort.bam", "56720_WT_T1_WT_10d_2.bam.sort.fastq.unmapped.sam.sort.bam", "56719_WT_T1_WT_10d_1.bam.sort.fastq.unmapped.sam.sort.bam", "56718_WT_T1_WT_0d_3.bam.sort.fastq.unmapped.sam.sort.bam", "56717_WT_T1_WT_0d_2.bam.sort.fastq.unmapped.sam.sort.bam", "56716_WT_T1_WT_0d_1.bam.sort.fastq.unmapped.sam.sort.bam", "56715_WT_T1_WT_6d_3.bam.sort.fastq.unmapped.sam.sort.bam", "56714_WT_T1_WT_6d_2.bam.sort.fastq.unmapped.sam.sort.bam", "56713_WT_T1_WT_6d_1.bam.sort.fastq.unmapped.sam.sort.bam", "56712_WT_T1_WT_0d_3.bam.sort.fastq.unmapped.sam.sort.bam", "56711_WT_T1_WT_0d_2.bam.sort.fastq.unmapped.sam.sort.bam", "56710_WT_T1_WT_0d_1.bam.sort.fastq.unmapped.sam.sort.bam", "56709_WT_T1_WT_0d_3.bam.sort.fastq.unmapped.sam.sort.bam", "56708_WT_T1_WT_0d_2.bam.sort.fastq.unmapped.sam.sort.bam", "56707_WT_T1_WT_0d_1.bam.sort.fastq.unmapped.sam.sort.bam", "56706_WT_T1_tt_0d_3.bam.sort.fastq.unmapped.sam.sort.bam", "56705_WT_T1_tt_0d_2.bam.sort.fastq.unmapped.sam.sort.bam", "56704_WT_T1_tt_0d_1.bam.sort.fastq.unmapped.sam.sort.bam")</span>
+<span class="co1"># header.new <- c("T17_Dry_Naturally_Freezedryseed", "T17_Dry_Naturally_Freezedryseed.1", "T17_Dry_Naturally_Freezedryseed.2", "T16_Dry_6days_Freezeafter6dageing", "T16_Dry_6days_Freezeafter6dageing.1", "T16_Dry_6days_Freezeafter6dageing.2", "T15_Dry_0days_Freezedryseed", "T15_Dry_0days_Freezedryseed.1", "T15_Dry_0days_Freezedryseed.2", "T14_Dry_10days_Freezeafter10dageing", "T14_Dry_10days_Freezeafter10dageing.1", "T14_Dry_10days_Freezeafter10dageing.2", "T13_Dry_6days_Freezeafter6dageing", "T13_Dry_6days_Freezeafter6dageing.1", "T13_Dry_6days_Freezeafter6dageing.2", "T12_Dry_0days_Freezedryseed", "T12_Dry_0days_Freezedryseed.1", "T12_Dry_0days_Freezedryseed.2", "T11_Imbibe_6days_12h", "T11_Imbibe_6days_12h.1", "T11_Imbibe_6days_12h.2", "T10_Imbibe_6days_5h", "T10_Imbibe_6days_5h.1", "T10_Imbibe_6days_5h.2", "T9_Imbibe_0dyas_5h", "T9_Imbibe_0dyas_5h.1", "T9_Imbibe_0dyas_5h.2", "T8_Imbibe_Naturally_47h", "T8_Imbibe_Naturally_47h.1", "T8_Imbibe_Naturally_47h.2", "T7_Imbibe_Naturally_24h", "T7_Imbibe_Naturally_24h.1", "T7_Imbibe_Naturally_24h.2", "T6_Imbibe_10days_72h", "T6_Imbibe_10days_72h.1", "T6_Imbibe_10days_72h.2", "T5_Imbibe_10days_24h", "T5_Imbibe_10days_24h.1", "T5_Imbibe_10days_24h.2", "T4_Imbibe_6days_47h", "T4_Imbibe_6days_47h.1", "T4_Imbibe_6days_47h.2", "T3_Imbibe_6days_24h", "T3_Imbibe_6days_24h.1", "T3_Imbibe_6days_24h.2", "T2_Imbibe_0days_24h", "T2_Imbibe_0days_24h.1", "T2_Imbibe_0days_24h.2", "T1_Imbibe_0days_5h", "T1_Imbibe_0days_5h.1", "T1_Imbibe_0days_5h.2")</span>
+<span class="co1"># </span>
+<span class="co1"># header.new <- header.new[order(header.ori)]</span>
+<span class="co1"># header.ori <- header.ori[order(header.ori)]</span>
+<span class="co1"># </span>
+<span class="co1"># col.header <- header.new</span>
+<span class="co1"># </span>
+<span class="co1"># colnames(data.rpkm) <- col.header</span>
+
+<a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/library.html"><span class="kw2">library</span></a><span class="br0">(</span><span class="st0">"DESeq2"</span><span class="br0">)</span>
+<a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/library.html"><span class="kw2">library</span></a><span class="br0">(</span><span class="st0">"ggplot2"</span><span class="br0">)</span>
+<a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/library.html"><span class="kw2">library</span></a><span class="br0">(</span><span class="st0">"RColorBrewer"</span><span class="br0">)</span>
+<a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/library.html"><span class="kw2">library</span></a><span class="br0">(</span><span class="st0">"pheatmap"</span><span class="br0">)</span>
+<a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/library.html"><span class="kw2">library</span></a><span class="br0">(</span><span class="st0">"BiocGenerics"</span><span class="br0">)</span>
+<a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/library.html"><span class="kw2">library</span></a><span class="br0">(</span><span class="st0">"rgl"</span><span class="br0">)</span>
+<a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/library.html"><span class="kw2">library</span></a><span class="br0">(</span><span class="st0">"magick"</span><span class="br0">)</span>
+<a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/library.html"><span class="kw2">library</span></a><span class="br0">(</span><span class="st0">"sjmisc"</span><span class="br0">)</span>
+
+
+<span class="co1">################### running ######################</span>
+<span class="co1">### PCA RPKM ###</span>
+
+<a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/set.seed.html"><span class="kw2">set.<span class="me1">seed</span></span></a><span class="br0">(</span><span class="nu0">0</span><span class="br0">)</span>
+
+data.<span class="me1">inv</span> <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/t.html"><span class="kw2">t</span></a><span class="br0">(</span>data.<span class="me1">rpkm</span><span class="br0">)</span>
+data.<span class="me1">dist</span> <span class="sy0"><-</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/stats/html/dist.html"><span class="kw7">dist</span></a><span class="br0">(</span>data.<span class="me1">inv</span>, method<span class="sy0">=</span><span class="st0">"euclidean"</span><span class="br0">)</span> <span class="co1"># "euclidean", "maximum", "manhattan", "canberra", "binary" or "minkowski"</span>
+data.<span class="me1">dist</span>.<span class="me1">hc</span> <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/stats/html/hclust.html"><span class="kw7">hclust</span></a><span class="br0">(</span>data.<span class="me1">dist</span>,method<span class="sy0">=</span><span class="st0">"ward.D2"</span><span class="br0">)</span>
+data.<span class="me1">dist</span>.<span class="me1">pca</span> <span class="sy0"><-</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/stats/html/princomp.html"><span class="kw7">princomp</span></a><span class="br0">(</span>data.<span class="me1">dist</span>,<a href="http://stat.ethz.ch/R-manual/R-devel/library/stats/html/cor.html"><span class="kw7">cor</span></a><span class="sy0">=</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/T.html"><span class="kw2">T</span></a><span class="br0">)</span>
+
+pc1 <span class="sy0"><-</span> data.<span class="me1">dist</span>.<span class="me1">pca</span>$scores<span class="br0">[</span>,<span class="nu0">1</span><span class="br0">]</span>
+pc2 <span class="sy0"><-</span> data.<span class="me1">dist</span>.<span class="me1">pca</span>$scores<span class="br0">[</span>,<span class="nu0">2</span><span class="br0">]</span>
+pc3 <span class="sy0"><-</span> data.<span class="me1">dist</span>.<span class="me1">pca</span>$scores<span class="br0">[</span>,<span class="nu0">3</span><span class="br0">]</span>
+
+<span class="co1"># create data frame for pc1 pc2 pc3</span>
+data.<span class="me1">dist</span>.<span class="me1">pca</span>.<span class="me1">frame</span> <span class="sy0">=</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/data.frame.html"><span class="kw2">data.<span class="me1">frame</span></span></a><span class="br0">(</span>pc1,pc2,pc3<span class="br0">)</span>
+<a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/rownames.html"><span class="kw2">rownames</span></a><span class="br0">(</span>data.<span class="me1">dist</span>.<span class="me1">pca</span>.<span class="me1">frame</span><span class="br0">)</span> <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/names.html"><span class="kw2">names</span></a><span class="br0">(</span>data.<span class="me1">dist</span>.<span class="me1">pca</span>$scale<span class="br0">)</span>
+<a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/colnames.html"><span class="kw2">colnames</span></a><span class="br0">(</span>data.<span class="me1">dist</span>.<span class="me1">pca</span>.<span class="me1">frame</span><span class="br0">)</span> <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span><span class="st0">"pc1"</span>,<span class="st0">"pc2"</span>,<span class="st0">"pc3"</span><span class="br0">)</span>
+
+condition.<span class="me1">values</span> <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span><span class="br0">)</span>
+condition.<span class="me1">values</span>.<span class="me1">color</span> <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span><span class="br0">)</span>
+
+
+<a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/for.html"><span class="kw2">for</span></a><span class="br0">(</span>a <span class="kw1">in</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/colnames.html"><span class="kw2">colnames</span></a><span class="br0">(</span>data.<span class="me1">rpkm</span><span class="br0">)</span><span class="br0">)</span> <span class="br0">{</span>
+
+ v <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/substr.html"><span class="kw2">substr</span></a><span class="br0">(</span>a, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/nchar.html"><span class="kw2">nchar</span></a><span class="br0">(</span>a<span class="br0">)</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/nchar.html"><span class="kw2">nchar</span></a><span class="br0">(</span>a<span class="br0">)</span><span class="br0">)</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/if.html"><span class="kw2">if</span></a><span class="br0">(</span>str_contains<span class="br0">(</span>v, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span><span class="nu0">1</span>,<span class="nu0">2</span>,<span class="nu0">3</span>,<span class="nu0">4</span>,<span class="nu0">5</span>,<span class="nu0">6</span>,<span class="nu0">7</span>,<span class="nu0">8</span>,<span class="nu0">9</span>,<span class="nu0">0</span><span class="br0">)</span>, logic <span class="sy0">=</span> <span class="st0">"or"</span><span class="br0">)</span><span class="br0">)</span> <span class="br0">{</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/if.html"><span class="kw2">if</span></a> <span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/substr.html"><span class="kw2">substr</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/substr.html"><span class="kw2">substr</span></a><span class="br0">(</span>a, <span class="nu0">1</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/nchar.html"><span class="kw2">nchar</span></a><span class="br0">(</span>a<span class="br0">)</span><span class="sy0">-</span><span class="nu0">2</span><span class="br0">)</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/nchar.html"><span class="kw2">nchar</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/substr.html"><span class="kw2">substr</span></a><span class="br0">(</span>a, <span class="nu0">1</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/nchar.html"><span class="kw2">nchar</span></a><span class="br0">(</span>a<span class="br0">)</span><span class="sy0">-</span><span class="nu0">2</span><span class="br0">)</span><span class="br0">)</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/nchar.html"><span class="kw2">nchar</span></a><span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/substr.html"><span class="kw2">substr</span></a><span class="br0">(</span>a, <span class="nu0">1</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/nchar.html"><span class="kw2">nchar</span></a><span class="br0">(</span>a<span class="br0">)</span><span class="sy0">-</span><span class="nu0">2</span><span class="br0">)</span><span class="br0">)</span><span class="br0">)</span> <span class="sy0">==</span> <span class="st0">"."</span><span class="br0">)</span> <span class="br0">{</span>
+ n <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/substr.html"><span class="kw2">substr</span></a><span class="br0">(</span>a, <span class="nu0">1</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/nchar.html"><span class="kw2">nchar</span></a><span class="br0">(</span>a<span class="br0">)</span><span class="sy0">-</span><span class="nu0">3</span><span class="br0">)</span>
+ <span class="br0">}</span> <span class="kw1">else</span> <span class="br0">{</span>
+ n <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/substr.html"><span class="kw2">substr</span></a><span class="br0">(</span>a, <span class="nu0">1</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/nchar.html"><span class="kw2">nchar</span></a><span class="br0">(</span>a<span class="br0">)</span><span class="sy0">-</span><span class="nu0">2</span><span class="br0">)</span>
+ <span class="br0">}</span>
+
+ <span class="br0">}</span> <span class="kw1">else</span> <span class="br0">{</span>
+ n <span class="sy0"><-</span> a
+
+ <span class="br0">}</span>
+ condition.<span class="me1">values</span> <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span>condition.<span class="me1">values</span>, librariesName<span class="br0">[</span>n<span class="br0">]</span><span class="br0">[</span><span class="br0">[</span><span class="nu0">1</span><span class="br0">]</span><span class="br0">]</span><span class="br0">[</span><span class="nu0">1</span><span class="br0">]</span><span class="br0">)</span>
+ condition.<span class="me1">values</span>.<span class="me1">color</span> <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span>condition.<span class="me1">values</span>.<span class="me1">color</span>, librariesName<span class="br0">[</span>n<span class="br0">]</span><span class="br0">[</span><span class="br0">[</span><span class="nu0">1</span><span class="br0">]</span><span class="br0">]</span><span class="br0">[</span><span class="nu0">2</span><span class="br0">]</span><span class="br0">)</span>
+<span class="br0">}</span>
+
+
+data.<span class="me1">dist</span>.<span class="me1">pca</span>.<span class="me1">frame</span><span class="br0">[</span><span class="st0">"tissue"</span><span class="br0">]</span> <span class="sy0"><-</span> condition.<span class="me1">values</span>
+data.<span class="me1">dist</span>.<span class="me1">pca</span>.<span class="me1">frame</span><span class="br0">[</span><span class="st0">"color"</span><span class="br0">]</span> <span class="sy0"><-</span> condition.<span class="me1">values</span>.<span class="me1">color</span>
+data.<span class="me1">dist</span>.<span class="me1">pca</span>.<span class="me1">frame</span><span class="br0">[</span><span class="st0">"name"</span><span class="br0">]</span> <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/names.html"><span class="kw2">names</span></a><span class="br0">(</span>data.<span class="me1">dist</span>.<span class="me1">pca</span>$scale<span class="br0">)</span>
+<a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/attr.html"><span class="kw2">attr</span></a><span class="br0">(</span>data.<span class="me1">dist</span>.<span class="me1">pca</span>.<span class="me1">frame</span>, <span class="st0">"percentVar"</span><span class="br0">)</span> <span class="sy0"><-</span> <span class="br0">(</span>data.<span class="me1">dist</span>.<span class="me1">pca</span>$sdev<span class="br0">)</span><span class="sy0">^</span><span class="nu0">2</span> <span class="sy0">/</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/sum.html"><span class="kw2">sum</span></a><span class="br0">(</span>data.<span class="me1">dist</span>.<span class="me1">pca</span>$sdev<span class="sy0">^</span><span class="nu0">2</span><span class="br0">)</span> <span class="co1"># cumsum()</span>
+
+<span class="co1"># simple plot</span>
+<a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/png.html"><span class="kw5">png</span></a><span class="br0">(</span>filename<span class="sy0">=</span>paste0<span class="br0">(</span>saveat, <span class="st0">"/HC_RPKM_normalized.png"</span><span class="br0">)</span><span class="br0">)</span>
+<a href="http://stat.ethz.ch/R-manual/R-devel/library/graphics/html/plot.html"><span class="kw4">plot</span></a><span class="br0">(</span>data.<span class="me1">dist</span>.<span class="me1">hc</span><span class="br0">)</span> <span class="co1"># hc plot</span>
+<a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/dev.off.html"><span class="kw5">dev.<span class="me1">off</span></span></a><span class="br0">(</span><span class="br0">)</span>
+<a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/png.html"><span class="kw5">png</span></a><span class="br0">(</span>filename<span class="sy0">=</span>paste0<span class="br0">(</span>saveat, <span class="st0">"/PCA_variance_RPKM_normalized.png"</span><span class="br0">)</span><span class="br0">)</span>
+<a href="http://stat.ethz.ch/R-manual/R-devel/library/graphics/html/plot.html"><span class="kw4">plot</span></a><span class="br0">(</span>data.<span class="me1">dist</span>.<span class="me1">pca</span><span class="br0">)</span> <span class="co1"># variances; var(data.dist.pca$sdev[1:9])</span>
+<a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/dev.off.html"><span class="kw5">dev.<span class="me1">off</span></span></a><span class="br0">(</span><span class="br0">)</span>
+<span class="co1"># get the parcent variation</span>
+percentVar <span class="sy0"><-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/round.html"><span class="kw2">round</span></a><span class="br0">(</span><span class="nu0">100</span> <span class="sy0">*</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/attr.html"><span class="kw2">attr</span></a><span class="br0">(</span>data.<span class="me1">dist</span>.<span class="me1">pca</span>.<span class="me1">frame</span>, <span class="st0">"percentVar"</span><span class="br0">)</span><span class="br0">)</span>
+
+<span class="co1"># 3d plot</span>
+plot3d<span class="br0">(</span>pc1, pc2, pc3,
+ type <span class="sy0">=</span> <span class="st0">"s"</span>, <span class="co1"># p, s, l, h, n</span>
+ <span class="co1">#pch = c(1:3),</span>
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/col.html"><span class="kw2">col</span></a> <span class="sy0">=</span> condition.<span class="me1">values</span>.<span class="me1">color</span>,
+ size <span class="sy0">=</span> <span class="nu0">1</span>,
+ xlab <span class="sy0">=</span> paste0<span class="br0">(</span><span class="st0">"PC1: "</span>,percentVar<span class="br0">[</span><span class="nu0">1</span><span class="br0">]</span>,<span class="st0">"% variance"</span><span class="br0">)</span>,
+ ylab <span class="sy0">=</span> paste0<span class="br0">(</span><span class="st0">"PC2: "</span>,percentVar<span class="br0">[</span><span class="nu0">2</span><span class="br0">]</span>,<span class="st0">"% variance"</span><span class="br0">)</span>,
+ zlab <span class="sy0">=</span> paste0<span class="br0">(</span><span class="st0">"PC3: "</span>,percentVar<span class="br0">[</span><span class="nu0">3</span><span class="br0">]</span>,<span class="st0">"% variance"</span><span class="br0">)</span>,
+ cex <span class="sy0">=</span> <span class="nu0">2</span>,
+ main <span class="sy0">=</span> <span class="st0">""</span>, <span class="co1"># -> princomp",</span>
+<span class="br0">)</span>
+
+<span class="co1"># shift <- matrix(4, 4, 4, byrow = TRUE)</span>
+<span class="co1"># text3d(shift,texts=1:3)</span>
+grid3d<span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span><span class="st0">"x"</span>, <span class="st0">"y"</span>, <span class="st0">"z"</span><span class="br0">)</span><span class="br0">)</span>
+
+<span class="co1">## add legend</span>
+legend3d<span class="br0">(</span><span class="st0">"right"</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/unique.html"><span class="kw2">unique</span></a><span class="br0">(</span>condition.<span class="me1">values</span><span class="br0">)</span>, pch <span class="sy0">=</span> <span class="nu0">19</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/col.html"><span class="kw2">col</span></a> <span class="sy0">=</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/unique.html"><span class="kw2">unique</span></a><span class="br0">(</span>condition.<span class="me1">values</span>.<span class="me1">color</span><span class="br0">)</span><span class="br0">)</span>
+
+<span class="co1">#### video #####</span>
+M <span class="sy0"><-</span> par3d<span class="br0">(</span><span class="st0">"userMatrix"</span><span class="br0">)</span>
+play3d<span class="br0">(</span> par3dinterp<span class="br0">(</span> userMatrix<span class="sy0">=</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/list.html"><span class="kw2">list</span></a><span class="br0">(</span>M,
+ rotate3d<span class="br0">(</span>M, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/pi.html"><span class="kw2">pi</span></a><span class="sy0">/</span><span class="nu0">2</span>, <span class="nu0">1</span>, <span class="nu0">0</span>, <span class="nu0">0</span><span class="br0">)</span>,
+ rotate3d<span class="br0">(</span>M, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/pi.html"><span class="kw2">pi</span></a><span class="sy0">/</span><span class="nu0">2</span>, <span class="nu0">0</span>, <span class="nu0">1</span>, <span class="nu0">0</span><span class="br0">)</span> <span class="br0">)</span> <span class="br0">)</span>,
+ duration<span class="sy0">=</span><span class="nu0">2</span> <span class="br0">)</span>
+
+movie3d<span class="br0">(</span>spin3d<span class="br0">(</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/graphics/html/axis.html"><span class="kw4">axis</span></a> <span class="sy0">=</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span><span class="nu0">1</span>, <span class="nu0">2</span>, <span class="nu0">1</span><span class="br0">)</span><span class="br0">)</span>, duration <span class="sy0">=</span> <span class="nu0">5</span>,
+ <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/dir.html"><span class="kw2">dir</span></a> <span class="sy0">=</span> saveat<span class="br0">)</span>
+
+<span class="co1">#### video end ####</span>
+
+<span class="co1"># pc1, pc2</span>
+<a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/png.html"><span class="kw5">png</span></a><span class="br0">(</span>filename<span class="sy0">=</span>paste0<span class="br0">(</span>saveat, <span class="st0">"/PCA_RPKM_normalized.png"</span><span class="br0">)</span><span class="br0">)</span>
+ggplot<span class="br0">(</span>
+ data.<span class="me1">dist</span>.<span class="me1">pca</span>.<span class="me1">frame</span>,
+ aes<span class="br0">(</span>
+ pc1,
+ pc2,
+ color<span class="sy0">=</span>tissue<span class="br0">)</span>
+<span class="br0">)</span> <span class="sy0">+</span>
+ geom_point<span class="br0">(</span>size<span class="sy0">=</span><span class="nu0">2.5</span><span class="br0">)</span> <span class="sy0">+</span>
+ xlab<span class="br0">(</span>
+ paste0<span class="br0">(</span><span class="st0">"PC1: "</span>,percentVar<span class="br0">[</span><span class="nu0">1</span><span class="br0">]</span>,<span class="st0">"% variance"</span><span class="br0">)</span>
+ <span class="br0">)</span> <span class="sy0">+</span>
+ ylab<span class="br0">(</span>
+ paste0<span class="br0">(</span><span class="st0">"PC2: "</span>,percentVar<span class="br0">[</span><span class="nu0">2</span><span class="br0">]</span>,<span class="st0">"% variance"</span><span class="br0">)</span>
+ <span class="br0">)</span> <span class="sy0">+</span>
+ <span class="co1">#theme() + #, face="bold"</span>
+ scale_colour_manual<span class="br0">(</span>
+ values<span class="sy0">=</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">(</span><span class="st0">"red"</span>, <span class="st0">"blue"</span>, <span class="st0">"green"</span>, <span class="st0">"yellow"</span>, <span class="st0">"black"</span>, <span class="st0">"violet"</span><span class="br0">)</span> <span class="co1"># dodgerblue3</span>
+ <span class="br0">)</span> <span class="sy0">+</span>
+ ggtitle<span class="br0">(</span><span class="st0">"PCA of all samples (RPKM normalized)"</span><span class="br0">)</span> <span class="sy0">+</span>
+ theme<span class="br0">(</span>
+ plot.<span class="me1">title</span> <span class="sy0">=</span> element_text<span class="br0">(</span>lineheight<span class="sy0">=</span>.8<span class="br0">)</span>,
+ panel.<span class="me1">background</span> <span class="sy0">=</span> element_rect<span class="br0">(</span>fill <span class="sy0">=</span> <span class="st0">"gray95"</span><span class="br0">)</span>
+ <span class="br0">)</span>
+<a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/dev.off.html"><span class="kw5">dev.<span class="me1">off</span></span></a><span class="br0">(</span><span class="br0">)</span></pre>
+</dd></dl>
+
+ <!-- wikipage stop -->
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+
+ <div class="docInfo"><bdi>personal/haasf/2021/madland/rnaseqhoecker/3d_pca_plot_hoecker_20210527.r.txt</bdi> · Last modified: 2021/06/01 12:22 by <bdi>Fabian Haas</bdi></div>
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