This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA). The GeneSet class provides a common data structure for representing gene sets. The GeneColorSet class allows genes in a set to be associated with phenotypes. The GeneSetCollection class facilitates grouping together a list of related gene sets. The GeneIdentifierType class hierarchy reflects how genes are represented (e.g., Entrez versus symbol) in the gene set. mapIdentifiers provides a way to convert identifiers in a set from one type to another. The CollectionType class hierarchy reflects how the gene set was made, and can order genes into distinct sets or collections.
Written by Martin Morgan, Seth Falcon, Robert Gentleman. Maintainer: Biocore Team c/o BioC user list <firstname.lastname@example.org>
GeneSet, GeneColorSet GeneSetCollection
Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: annotate Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: IRanges Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:base': colMeans, colSums, expand.grid, rowMeans, rowSums Loading required package: XML Loading required package: graph Attaching package: 'graph' The following object is masked from 'package:XML': addNode GeneSt> ## Empty gene set GeneSt> GeneSet() setName: NA geneIds: (total: 0) geneIdType: Null collectionType: Null details: use 'details(object)' GeneSt> ## Gene set from ExpressionSet GeneSt> data(sample.ExpressionSet) GeneSt> gs1 <- GeneSet(sample.ExpressionSet[100:109]) GeneSt> ## GeneSet from Broad XML; 'fl' could be a url GeneSt> fl <- system.file("extdata", "Broad.xml", package="GSEABase") GeneSt> gs2 <- getBroadSets(fl)[] # actually, a list of two gene sets GeneSt> ## GeneSet from list of gene identifiers GeneSt> geneIds <- geneIds(gs2) # any character vector would do GeneSt> gs3 <- GeneSet(geneIds) GeneSt> ## unspecified set type, so... GeneSt> is(geneIdType(gs3), "NullIdentifier") == TRUE  TRUE GeneSt> ## update set type to match encoding of identifiers GeneSt> geneIdType(gs2) geneIdType: Symbol GeneSt> geneIdType(gs3) <- SymbolIdentifier() GeneSt> ## other ways of accomplishing the same GeneSt> gs4 <- GeneSet(geneIds, geneIdType=SymbolIdentifier()) GeneSt> gs5 <- GeneSet(SymbolIdentifier(), geneIds=geneIds)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.