From 688bc7c96f2af6164ff5d926de92d019793112f7 Mon Sep 17 00:00:00 2001
From: Holger Brandl <brandl@mpi-cbg.de>
Date: Tue, 10 Mar 2015 16:01:15 +0100
Subject: [PATCH] added more ontologies
---
R/bio/diffex_commons.R | 6 +++++-
1 file changed, 5 insertions(+), 1 deletion(-)
diff --git a/R/bio/diffex_commons.R b/R/bio/diffex_commons.R
index 6144e5a..e0c0981 100644
--- a/R/bio/diffex_commons.R
+++ b/R/bio/diffex_commons.R
@@ -136,7 +136,7 @@ rintersect.list <- function(LDF){
## http://www.bioconductor.org/packages/release/bioc/vignettes/RDAVIDWebService/inst/doc/RDavidWS-vignette.pdf
## e.g. getClusterReport --> plot2D
-DEF_DAVID_ONTOLOGIES=ontologies=c("GOTERM_CC_FAT", "GOTERM_MF_FAT", "GOTERM_BP_FAT", "PANTHER_PATHWAY", "REACTOME_PATHWAY", "KEGG_PATHWAY", "GOTERM_CC_FAT", "GOTERM_MF_FAT", "GOTERM_BP_FAT")
+DEF_DAVID_ONTOLOGIES=ontologies=c("GOTERM_CC_FAT", "GOTERM_MF_FAT", "GOTERM_BP_FAT", "PANTHER_PATHWAY", "PANTHER_FAMILY", "PANTHER_PATHWAY", "KEGG_PATHWAY", "REACTOME_PATHWAY")
davidAnnotationChart <- function( someGenes, ontologies=DEF_DAVID_ONTOLOGIES ){
@@ -153,6 +153,10 @@ davidAnnotationChart <- function( someGenes, ontologies=DEF_DAVID_ONTOLOGIES ){
david<-DAVIDWebService$new(email="brandl@mpi-cbg.de")
+# ## list all ontologies
+# getAllAnnotationCategoryNames(david)
+
+
# getTimeOut(david)
setTimeOut(david, 80000) ## http://www.bioconductor.org/packages/release/bioc/vignettes/RDAVIDWebService/inst/doc/RDavidWS-vignette.pdf
--
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