filtering in GSEABase package
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jason0701 ▴ 190
@jason0701-3921
Last seen 2.2 years ago
Hi All, I noticed a problem which I am not sure if I miss something. I attempt to select GO terms in the biological process categories (BP). But for some reasons the filtering seems not working. One id is in the MF category, but still is selected (see below). library(GSEABase) data(sample.ExpressionSet) gg <- GeneSetCollection(sample.ExpressionSet[200:250], setType = GOCollection(ontology="BP")) goId = "GO:0003676" # is in MF, not in BP goId %in% names(gg) TRUE > sessionInfo() R version 2.10.0 (2009-10-26) x86_64-redhat-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] hgu95av2.db_2.3.5 org.Hs.eg.db_2.3.6 KEGG.db_2.3.5 [4] Category_2.12.0 GO.db_2.3.5 GSEABase_1.8.0 [7] graph_1.24.1 annotate_1.24.0 mouse4302.db_2.3.5 [10] org.Mm.eg.db_2.3.6 RSQLite_0.7-3 DBI_0.2-5 [13] AnnotationDbi_1.8.1 genefilter_1.28.2 ALL_1.4.7 [16] Biobase_2.6.1 loaded via a namespace (and not attached): [1] RBGL_1.22.0 splines_2.10.0 survival_2.35-7 tools_2.10.0 [5] XML_2.6-0 xtable_1.5-6 > Thanks for looking into this. Jason
GO hgu95av2 mouse4302 PROcess Category GO hgu95av2 mouse4302 PROcess Category • 669 views
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James F. Reid ▴ 610
@james-f-reid-3148
Last seen 7.4 years ago
Hi Jason, the help page of GeneSetCollection specifies that using 'ontology' does work like 'evidence' where filtering is taking place. You could filter out your results using GOTERM (GO.db) in this way: goId %in% names(gg[lapply(mget(names(gg), GOTERM), Ontology) == "MF"]) ##[1] TRUE goId %in% names(gg[lapply(mget(names(gg), GOTERM), Ontology) == "BP"]) HTH, J. On 29/03/2010 18:41, Jason Lu wrote: > Hi All, > > I noticed a problem which I am not sure if I miss something. > > I attempt to select GO terms in the biological process categories > (BP). But for some reasons the filtering seems not working. One id is > in the MF category, but still is selected (see below). > > > library(GSEABase) > data(sample.ExpressionSet) > gg<- GeneSetCollection(sample.ExpressionSet[200:250], > setType = GOCollection(ontology="BP")) > > goId = "GO:0003676" # is in MF, not in BP > > goId %in% names(gg) > TRUE > >> sessionInfo() > R version 2.10.0 (2009-10-26) > x86_64-redhat-linux-gnu > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] hgu95av2.db_2.3.5 org.Hs.eg.db_2.3.6 KEGG.db_2.3.5 > [4] Category_2.12.0 GO.db_2.3.5 GSEABase_1.8.0 > [7] graph_1.24.1 annotate_1.24.0 mouse4302.db_2.3.5 > [10] org.Mm.eg.db_2.3.6 RSQLite_0.7-3 DBI_0.2-5 > [13] AnnotationDbi_1.8.1 genefilter_1.28.2 ALL_1.4.7 > [16] Biobase_2.6.1 > > loaded via a namespace (and not attached): > [1] RBGL_1.22.0 splines_2.10.0 survival_2.35-7 tools_2.10.0 > [5] XML_2.6-0 xtable_1.5-6 >> > > Thanks for looking into this. > > Jason > > _______________________________________________ > 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 >
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