diff --git a/R/bio/diffex_commons.R b/R/bio/diffex_commons.R index 6144e5a509c3b02813fcf0ada4f6ca6b477508c4..e0c0981808ad14b19d8cc4eef6b369428d6e5bb7 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