Hi burak -- burak kutlu <burak_kutlu at="" yahoo.com=""> writes: > Hello > I am trying to apply a function to each element of a > GeneSetCollection object. I have a problem preserving the data > class, if I use lapply(). Is using a for loop my only option? I think what you want to do is put the result (a list of gene sets) back into a gene set collection > example(GeneSetCollection) [snip] > gsc GeneSetCollection names: GO:0000187, GO:0000398, ..., GO:0046872 (156 total) unique identifiers: 31445_at, 31463_s_at, ..., 31441_at (40 total) types in collection: geneIdType: AnnotationIdentifier (1 total) collectionType: GOCollection (1 total) > GeneSetCollection(lapply(gsc, function(f) { geneIds(f) <- "burak"; f })) GeneSetCollection names: GO:0000187, GO:0000398, ..., GO:0046872 (156 total) unique identifiers: burak (1 total) types in collection: geneIdType: AnnotationIdentifier (1 total) collectionType: GOCollection (1 total) In some special cases GeneSetCollection 'knows' how to do some things, see the results of > showMethods(class="GeneSetCollection", where=getNamespace("GSEABase")) and > ?"GeneSetCollection-class" for instance, > mapIdentifiers(gsc, EntrezIdentifier()) GeneSetCollection names: GO:0000187, GO:0000398, ..., GO:0046872 (156 total) unique identifiers: 6464, 3178, ..., 643332 (35 total) types in collection: geneIdType: EntrezIdentifier (1 total) collectionType: GOCollection (1 total) Martin > Thanks for any help > -burak > > Here's what I do: > >> gsc > GeneSetCollection > names: chr16q, chr5q23, ..., INOSITOL_OR_PHOSPHATIDYLINOSITOL_KINASE_ACTIVITY (5452 total) > unique identifiers: CMAR, USP10, ..., UCHL5IP (39655 total) > types in collection: > geneIdType: SymbolIdentifier (1 total) > collectionType: BroadCollection (1 total) > >> test1 = GeneSetCollection(gsc[[1]],gsc[[2]]) >> test1 > GeneSetCollection > names: chr16q, chr5q23 (2 total) > unique identifiers: CMAR, USP10, ..., LOC728586 (91 total) > types in collection: > geneIdType: SymbolIdentifier (1 total) > collectionType: BroadCollection (1 total) > >> lapply(test1,function(f) {geneIds(f) = "burak";return(f)}) > [[1]] > setName: chr16q > geneIds: burak (total: 1) > geneIdType: Symbol > collectionType: Broad > bcCategory: c1 (Positional) > bcSubCategory: NA > details: use 'details(object)' > > [[2]] > setName: chr5q23 > geneIds: burak (total: 1) > geneIdType: Symbol > collectionType: Broad > bcCategory: c1 (Positional) > bcSubCategory: NA > details: use 'details(object)' > > ## returns a list > >> sessionInfo() > R version 2.8.0 (2008-10-20) > x86_64-unknown-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC _NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDEN TIFICATION=C > > attached base packages: > [1] grDevices datasets splines graphics stats utils tools > [8] methods base > > other attached packages: > [1] org.Hs.eg.db_2.2.6 RSQLite_0.7-1 GSEABase_1.4.0 > [4] graph_1.20.0 annotate_1.20.0 xtable_1.5-4 > [7] AnnotationDbi_1.4.1 RMySQL_0.6-1 DBI_0.2-4 > [10] simpleaffy_2.18.0 gcrma_2.14.1 matchprobes_1.14.0 > [13] genefilter_1.22.0 survival_2.34-1 affy_1.20.0 > [16] Biobase_2.2.0 > > loaded via a namespace (and not attached): > [1] affyio_1.10.1 cluster_1.11.11 preprocessCore_1.4.0 > [4] XML_1.98-1 > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793