GSEABase-package: Gene set enrichment data structures and methods

In GSEABase: Gene set enrichment data structures and methods

Description

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.

Author(s)

Written by Martin Morgan, Seth Falcon, Robert Gentleman. Maintainer: Biocore Team c/o BioC user list <[e-mail]>

See Also

GeneSet, GeneColorSet GeneSetCollection

Examples

example(GeneSet)

Example output

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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)[[1]] # 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
[1] 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)

GSEABase documentation built on Dec. 13, 2020, 2 a.m.