Fixes #135, check for number of variables in sample_type

BIMSBbioinfo · Nov 7, 2023 · 80ee4c9 · 80ee4c9
1 parent da0c584
commit 80ee4c9
Showing 1 changed file with 5 additions and 1 deletion.
diff --git a/scripts/counts_matrix_from_SALMON.R b/scripts/counts_matrix_from_SALMON.R
@@ -37,7 +37,11 @@ writeCounts <- function(colDataFile, salmon_output_folder, counts_dir, type) {
   names(files) <- rownames(colData)
   txi <- tximport::tximport(files, type = "salmon", txOut = TRUE)
 
-  dds <- DESeq2::DESeqDataSetFromTximport(txi, colData, ~group)
+  if(length(unique(colData$sample_type)) < 2) {
+    dds <- DESeq2::DESeqDataSetFromTximport(txi, colData, ~1)
+  } else {
+    dds <- DESeq2::DESeqDataSetFromTximport(txi, colData, ~group)
+  }
 
   #save raw counts
   write.table(x = DESeq2::counts(dds),