On 04/16/2015 04:57 PM, Steve Lianoglou wrote:
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.
Thanks Steve, this will appear in 1.30.1 (release) and 1.31.1.
Martin
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
--
Computational Biology / Fred Hutchinson Cancer Research Center
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