[Bioc-devel] Update GSEABase to support new MSigDB collection in v5.0
Steve Lianoglou
lianoglou.steve at gene.com
Fri Apr 17 01:57:50 CEST 2015
Howdy,
It was recently brought to my attention that there is a new "h"
collection in MSigDB v5.0:
http://www.broadinstitute.org/gsea/msigdb/genesets.jsp?collection=H
Here's a diff against RELEASE that I think should do the trick. There
are some spurious +/- entries here because (I think) my editor trims
whitespace on save.
Anyway, this should orient you to where you have to make these changes
quickly enough, I'd imagine:
Index: GSEABase/R/methods-CollectionType.R
===================================================================
--- GSEABase/R/methods-CollectionType.R (revision 102608)
+++ GSEABase/R/methods-CollectionType.R (working copy)
@@ -70,7 +70,7 @@
BroadCollection <- function(category="c1", subCategory=NA, ...) {
if (length(category)!=1 ||
- !(category %in% c("c1", "c2", "c3", "c4", "c5", "c6", "c7")))
+ !(category %in% c("c1", "c2", "c3", "c4", "c5", "c6", "c7", "h")))
stop(sprintf("invalid BroadCollection category: '%s'",
paste(category, collapse="', '")))
new("BroadCollection",
@@ -93,9 +93,10 @@
c2="c2 (Curated)",
c3="c3 (Motif)",
c4="c4 (Computational)",
- c5="c5 (GO)",
+ c5="c5 (GO)",
c6="c6 (Oncogenic Pathway Activation Modules)",
- c7="c7 (Immunologic Signatures)"), "\n",
+ c7="c7 (Immunologic Signatures)"),
+ h="h (Hallmark)", "\n",
" bcSubCategory: ", bcSubCategory(object), "\n", sep="")
})
Thanks,
-steve
--
Steve Lianoglou
Computational Biologist
Genentech
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