[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


It was recently brought to my attention that there is a new "h"
collection in MSigDB v5.0:


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="', '")))
@@ -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="")


Steve Lianoglou
Computational Biologist

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