Dear all I'm working with an unsupported organism. However I have a table of PFAM annotations for my genes and would like to make a GeneSetCollection out of it (to use it later for hypergeometric testing etc...) So how would I get a data set like this: gene_id pfam_id XLOC_000002 PF00354 XLOC_000002 PF13385 XLOC_000005 PF10523 XLOC_000005 PF13385 XLOC_000007 PF00013 XLOC_000007 PF02791 XLOC_000007 PF13385 into a GeneSetCollection ?? Thanks, kind regards Fabian

Hi Fabian -- On 06/06/2014 06:28 AM, Fabian Grammes wrote: > Dear all > > I'm working with an unsupported organism. However I have a table > of PFAM annotations for my genes and would like to make a > GeneSetCollection out of it (to use it later for hypergeometric testing > etc...) > > So how would I get a data set like this: > > gene_id pfam_id > XLOC_000002 PF00354 > XLOC_000002 PF13385 > XLOC_000005 PF10523 > XLOC_000005 PF13385 > XLOC_000007 PF00013 > XLOC_000007 PF02791 > XLOC_000007 PF13385 > > into a GeneSetCollection ?? I read in your data df <- read.csv(textConnection("gene_id,pfam_id XLOC_000002,PF00354 XLOC_000002,PF13385 XLOC_000005,PF10523 XLOC_000005,PF13385 XLOC_000007,PF00013 XLOC_000007,PF02791 XLOC_000007,PF13385"), stringsAsFactors=FALSE, row.names=NULL) then split it into groups based on pfam identifier sets <- split(df$gene_id, df$pfam_id) then created one gene set for each pfam id, and collected the set into a collection library(GSEABase) gsc <- GeneSetCollection(Map(function(pid, gids) { GeneSet(gids, setName=pid, collectionType=PfamCollection(pid)) }, names(sets), sets)) resulting in > gsc GeneSetCollection names: PF00013, PF00354, ..., PF13385 (5 total) unique identifiers: XLOC_000007, XLOC_000002, XLOC_000005 (3 total) types in collection: geneIdType: NullIdentifier (1 total) collectionType: PfamCollection (1 total) > gsc[["PF13385"]] setName: PF13385 geneIds: XLOC_000002, XLOC_000005, XLOC_000007 (total: 3) geneIdType: Null collectionType: Pfam ids: PF13385 (1 total) details: use 'details(object)' Hope that helps, Martin > > Thanks, kind regards > > Fabian > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793