disabled duplicated export of diffex genes

dge_workflow/featcounts_deseq.R

@@ -406,8 +406,11 @@ degs <- deAnnot %>% filter(is_hit)
 #    inner_join(normCounts) %>%
 #    left_join(geneInfo) %>%
 #    left_join(bindCats)
-degs %>% write.delim(file=paste0(resultsBase, "diffex_genes.txt"))
-#'  [degs](`r paste0(resultsBase, "diffbind_genes.txt")`)
+degs %>% write_tsv(paste0(resultsBase, "diffex_genes.txt"))
+#' [Differentially Expressed Genes](`r paste0(resultsBase, "diffbind_genes.txt")`)
+
+#write.delim(degs, file="degs.txt")
+# degs <- read.delim("degs.txt")
 
 
 #unloadNamespace("dplyr"); require(dplyr)
@@ -450,9 +453,6 @@ degs %>% count( sample_1, sample_2, s1_overex) %>% kable()
 
 
 #'  DEGs (differentially expressed genes) are contained in the following table
-write.delim(degs, file="degs.txt")
-# degs <- read.delim("degs.txt")
-#' [Differentially Expressed Genes](degs.txt)
 
 
 #' DEGs can be browsed in Excel using the exported table or via the embedded table browser. To enable the IGV links, you need to set the port in the IGV preferences to 3334.