From 6c36180a6b8a196a3ec9b15fdeeef41751925db5 Mon Sep 17 00:00:00 2001
From: Holger Brandl <holgerbrandl@gmail.com>
Date: Mon, 21 Sep 2015 13:50:25 +0200
Subject: [PATCH] tweaked names in star count matrix aggregation
---
dge_workflow/dge_utils.sh | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/dge_workflow/dge_utils.sh b/dge_workflow/dge_utils.sh
index 38e4285..8d43570 100755
--- a/dge_workflow/dge_utils.sh
+++ b/dge_workflow/dge_utils.sh
@@ -459,14 +459,14 @@ devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v
exprCounts <- list.files(".", "ReadsPerGene.out.tab") %>% ldply(function(countFile){
read.delim(countFile, header=F) %>%
select(V1, V2) %>%
- set_names("gene_id", "num_alignments") %>%
- filter(!str_detect(gene_id, "^N_")) %>%
+ set_names("ensembl_gene_id", "num_alignments") %>%
+ filter(!str_detect(ensembl_gene_id, "^N_")) %>%
mutate(sample=trim_ext(countFile, ".ReadsPerGene.out.tab"))
}, .progress="text")
countMatrix <- spread(exprCounts, sample, num_alignments)
-write.delim(countMatrix, "star_count_matrix.txt")
+write.delim(countMatrix, "star_counts_matrix.txt")
' | R --vanilla -q
}
--
GitLab