From f5fd079ee8fd72074749d2a938ce4e7fcef172d5 Mon Sep 17 00:00:00 2001
From: Naharajan <dilln2002@gmail.com>
Date: Tue, 8 Mar 2016 15:24:54 +0100
Subject: [PATCH] replaced clusterProfiler::bitr to bitr while id conversion
---
common/cp_enrichment.R | 7 +++++--
1 file changed, 5 insertions(+), 2 deletions(-)
diff --git a/common/cp_enrichment.R b/common/cp_enrichment.R
index 3e7661f..d5a7fa8 100755
--- a/common/cp_enrichment.R
+++ b/common/cp_enrichment.R
@@ -128,8 +128,11 @@ annoDb <- guess_anno_db(geneLists$ensembl_gene_id) # e.g. "org.Hs.eg.db"
## convert to entrez gene ids
-glMappedRaw <- clusterProfiler::bitr(geneLists$ensembl_gene_id, fromType="ENSEMBL", toType="ENTREZID", annoDb=annoDb) %>%
- set_names("ensembl_gene_id", "entrez_gene_id") %>% right_join(geneLists)
+#glMappedRaw <- clusterProfiler::bitr(geneLists$ensembl_gene_id, fromType="ENSEMBL", toType="ENTREZID", annoDb=annoDb) %>%
+# set_names("ensembl_gene_id", "entrez_gene_id") %>% right_join(geneLists)
+
+glMappedRaw <- bitr(geneLists$ensembl_gene_id, fromType="ENSEMBL", toType="ENTREZID", annoDb=annoDb) %>%
+ set_names("ensembl_gene_id", "entrez_gene_id") %>% right_join(geneLists)
#' Check how many failed to map
--
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