diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000000000000000000000000000000000000..5b6a0652566d10360493952aec6d4a4febc77083 --- /dev/null +++ b/.gitignore @@ -0,0 +1,4 @@ +.Rproj.user +.Rhistory +.RData +.Ruserdata diff --git a/assays/cmQTL_val1_GH_2020_GC_MS/dataset/MAF_GC_MS.xlsx b/assays/cmQTL_val1_GH_2020_GC_MS/dataset/MAF_GC_MS.xlsx new file mode 100644 index 0000000000000000000000000000000000000000..7bd24a801baa7802164201f4c0d419330560a21d --- /dev/null +++ b/assays/cmQTL_val1_GH_2020_GC_MS/dataset/MAF_GC_MS.xlsx @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:418ee94bfb5c89f06b385367b042997416434a8b48b66d3adfa72aa100ea9af5 +size 27833 diff --git a/assays/cmQTL_val1_GH_2020_GC_MS/isa.assay.xlsx b/assays/cmQTL_val1_GH_2020_GC_MS/isa.assay.xlsx index 3525c21ed6eeb9204b5fcee96e88ba9acd8d5e71..46d812e8dea29a26a5a9ad136956fc45d8381765 100644 Binary files a/assays/cmQTL_val1_GH_2020_GC_MS/isa.assay.xlsx and b/assays/cmQTL_val1_GH_2020_GC_MS/isa.assay.xlsx differ diff --git a/cmQTL_val1_arc.Rproj b/cmQTL_val1_arc.Rproj new file mode 100644 index 0000000000000000000000000000000000000000..8e3c2ebc99e2e337f7d69948b93529a437590b27 --- /dev/null +++ b/cmQTL_val1_arc.Rproj @@ -0,0 +1,13 @@ +Version: 1.0 + +RestoreWorkspace: Default +SaveWorkspace: Default +AlwaysSaveHistory: Default + +EnableCodeIndexing: Yes +UseSpacesForTab: Yes +NumSpacesForTab: 2 +Encoding: UTF-8 + +RnwWeave: Sweave +LaTeX: pdfLaTeX diff --git a/studies/cmQTL_val1_GH_2020/isa.study.xlsx b/studies/cmQTL_val1_GH_2020/isa.study.xlsx index 96504e1767ca8a566955d1d32dfd904874b2f778..b165aaf2a3373c6687c8f5b762423c53619a8b20 100644 Binary files a/studies/cmQTL_val1_GH_2020/isa.study.xlsx and b/studies/cmQTL_val1_GH_2020/isa.study.xlsx differ diff --git a/workflows/GC_MS_normalization/210927_primary_normalization_with_split.R b/workflows/GC_MS_normalization/210927_primary_normalization_with_split.R index 641268852b0beaf65953ebe36dfd6c593c7cc97d..4a0e92ba6dac7cefaa98bf14e2b6478c1e3da928 100644 --- a/workflows/GC_MS_normalization/210927_primary_normalization_with_split.R +++ b/workflows/GC_MS_normalization/210927_primary_normalization_with_split.R @@ -1,9 +1,4 @@ rm(list = ls()) -#setwd(dirname(rstudioapi::getActiveDocumentContext()$path)) -#getwd() -#current <- getwd() -#source <- ".." - library(openxlsx) library(tidyverse) @@ -31,7 +26,6 @@ if (file.exists(out)) { dir.create(out) } setwd(here())# Not recommended but convenient in Rstudio to start from root -#out_dir <- str_c(current, out, sep = "/") # Data loading ------------------------------------------------------------