Fsharp cwl

workflows/deseq2/deseq2.R

@@ -6,13 +6,14 @@ library("DESeq2")
 library("tximport")
 library("rhdf5")
 library("ggplot2")
+library("readxl")
 
 ## In-and-out
 
-# inKallistoResults <- "../../runs/kallisto/kallisto_results"
-# inMetadataFile <- "../../runs/merged_isa_metadata/out/merged_isa.tsv"
-# inMetadataSample <- "Source.Name"
-# inMetadataFactorList <- list("Factor..Photosynthesis.mode.", "Factor..Biosource.amount.")
+inKallistoResults <- "../../runs/kallisto/kallisto_results"
+inMetadataFile <- "../../runs/isaSampleToRawDataSeq-run/rnaseq-samples.xlsx"
+inMetadataSample <- "Input [Source Name]"
+inMetadataFactorList <- list("Factor [Photosynthesis mode]")
 
 ### Read arguments from CLI
 
@@ -34,13 +35,18 @@ head(txi$counts)
 
 ## Read sample metadata
 
-samples_metadata <- read.table(file = inMetadataFile, sep = "\t")
+samples_metadata <- as.data.frame(read_xlsx(path = inMetadataFile))
 samples <- samples_metadata[order(samples_metadata[[inMetadataSample]]), c(inMetadataSample, unlist(inMetadataFactorList))]
+
 rownames(samples) <- samples[,inMetadataSample]
 
 factors <- sapply(inMetadataFactorList, function(x) x[[1]])
-design_formula <- as.formula(paste("~", paste(rev(factors), collapse = " + ")))
 
+## Annoying workaround to prevent formula error with special chars in column headers
+colnames(samples) <- make.names(colnames(samples))
+factors <- make.names(factors)
+
+design_formula <- as.formula(paste("~", paste(rev(factors), collapse = " + ")))
 
 ## DESeq