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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
