[Bioc-devel] Update GSEABase to support new MSigDB collection in v5.0

[Martin Morgan]

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
>


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