From f047009aebec3e36ba17ae26a0cd80a5c9aa4e3e Mon Sep 17 00:00:00 2001
From: Holger Brandl <holgerbrandl@gmail.com>
Date: Mon, 1 Feb 2016 09:24:50 +0100
Subject: [PATCH] disabled duplicated export of diffex genes
---
dge_workflow/featcounts_deseq.R | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/dge_workflow/featcounts_deseq.R b/dge_workflow/featcounts_deseq.R
index 089d4fc..157c0a7 100755
--- a/dge_workflow/featcounts_deseq.R
+++ b/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.
--
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