fixed replicate extraction pattern

dge_workflow/featcounts_deseq.R

@@ -87,7 +87,7 @@ genesAfter <- nrow(countMatrix)
 #' [Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2](http://genomebiology.com/2014/15/12/550/abstract)
 
 
-get_sample_from_replicate <- function(repName) str_match(repName, "(.*)_[R]?[0-9]{1}$")[,2]
+get_sample_from_replicate <- function(repName) str_match(repName, "(.*)_([R]|rep)?[0-9]{1}$")[,2]
 
 # Define or load a contrasts matrix
 if(!is.null(contrasts_file)){
@@ -117,7 +117,13 @@ contrasts %>% kable()
 colData <- data.frame(condition=colnames(countMatrix) %>% get_sample_from_replicate)
 
 # valiadate that contrasts model is compatible with data
-stopifnot(all((contrasts %>% gather %$% value %>% unique) %in% colData$condition))
+
+if(!all((contrasts %>% gather %$% value %>% unique) %in% colData$condition)){
+    echo("column model: ",colData$condition)
+    echo("contrasts: ", contrasts %>% gather %$% value %>% unique)
+    stop("column model is not consistent with contrasts")
+}
+#stopifnot(all((contrasts %>% gather %$% value %>% unique) %in% colData$condition))
 
 dds <- DESeqDataSetFromMatrix(countMatrix, colData, formula(~ condition))
 dds <- estimateSizeFactors(dds)