Hi all, I construct a GeneSetCollection objects from .gmt file using the following function TFT<-getGmt('c3.all.v3.0.entrez.gmt',geneIdType=EntrezIdentifier(),col lectionType=BroadCollection(category="c3")) I want to convert this GeneSetCollection object into a list with names identifying gene sets and each entry of the list containing the gene identifiers of the genes forming the corresponding set. I was wondering if there is a function doing that. I searched around and did not have any luck yet. I wonder if somebody knows the function for converting a GeneSetCollection to a list. Thank you very much. Wendy [[alternative HTML version deleted]]

hi Wendy, this is an easy one, your looking for the function geneIds() defined in the GSEABase package (thus you need to load this one as well, it gets automatically installed with GSVA). if you're likely to be handling GeneSetCollection objects here and there i recommend you to take a look to the Vignette "An Introduction to GSEABase" from the GSEABase package. cheers, robert. On Mon, 2011-11-14 at 20:44 -0500, Wendy Qiao wrote: > Hi all, > > I construct a GeneSetCollection objects from .gmt file using the following > function > > TFT<-getGmt('c3.all.v3.0.entrez.gmt',geneIdType=EntrezIdentifier(),c ollectionType=BroadCollection(category="c3")) > > I want to convert this GeneSetCollection object into a list with names > identifying gene sets and each entry of the list containing the gene > identifiers of the genes forming the corresponding set. I was wondering if > there is a function doing that. I searched around and did not have any luck > yet. I wonder if somebody knows the function for converting a > GeneSetCollection to a list. > > Thank you very much. > > Wendy > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 >