Fix #134

nf-core · Mar 17, 2022 · 9adca2f · 9adca2f
1 parent e5989ae
commit 9adca2f
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -20,6 +20,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Other enhancements & fixes
 
+* [#134](https://github.com/nf-core/smrnaseq/issues/134) - Fixed colSum of zero issues for edgeR_miRBase.R script
+
 ### Parameters
 
 | Old parameter                | New parameter              |

diff --git a/bin/edgeR_miRBase.r b/bin/edgeR_miRBase.r
@@ -41,11 +41,14 @@ for (i in 1:2) {
     # Remove genes with 0 reads in all samples
     row_sub = apply(data, 1, function(row) all(row ==0 ))
     # Only subset if at least one sample is remaining
-    nr_keep <- table(row_sub)
-    nr_keep <- sum(nr_keep == TRUE)
+    nr_keep <- sum(row_sub)
     if (nr_keep > 0){
         data<-data[!row_sub,]
     }
+
+    #Also check for colSums > 0, otherwise DGEList will fail if samples have entirely colSum == 0 #Fixes #134
+    drop_colsum_zero <- (colSums(data, na.rm=T) != 0) # T if colSum is not 0, F otherwise
+    data <- data[, drop_colsum_zero] # all the non-zero columns
 
     write.csv(t(data),file=paste(header,"_counts.csv",sep=""))