Merge pull request #77 from ywilke/bug_fix

Fixed an issue where the edgeR and DESeq2 task would fail when there is only 1 sample being run with the pipeline.
UMCUGenetics · Mar 3, 2021 · 76fad46 · 76fad46
2 parents 38d8e21 + 8745b8d
commit 76fad46
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diff --git a/bin/deseq2Normalize.R b/bin/deseq2Normalize.R
@@ -6,6 +6,7 @@ library("DESeq2")
 args = commandArgs(trailingOnly=TRUE)
 counts_raw <- read.delim(args[1], comment.char="#", row.names = 1)
 cds = as.matrix(counts_raw[,7:ncol(counts_raw)])
+colnames(cds) <- colnames(counts_raw)[7:ncol(counts_raw)]
 #Get column data and set dummy condition
 (colData <- data.frame(row.names=colnames(cds),condition=factor(c(rep("exp", ncol(cds))))))
 #Create DEseq2 dataset

diff --git a/bin/edgerNormalize.R b/bin/edgerNormalize.R
@@ -8,7 +8,8 @@ args = commandArgs(trailingOnly=TRUE)
 
 fc.df <- read.delim(args[1], comment.char="#")
 # Normalize 
-counts <- fc.df[,8:ncol(fc.df)]
+counts <- data.frame(fc.df[,8:ncol(fc.df)])
+colnames(counts) <- colnames(fc.df)[8:ncol(fc.df)]
 rownames(counts) <- fc.df$Geneid
 x <- DGEList(counts=counts, genes=fc.df[,c("Geneid","Length")] )
 # RPKM/CPM normalization