Load gene sets from files

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Description

This function is to load annotation of gene sets from files. The files are in the format of Molecular Signatures Database (MSigDB), and those files can be downloaded at http://www.broadinstitute.org/gsea/msigdb/index.jsp.

Usage

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loadGenesets(geneset.file, geneIDs, geneID.type = c("gene.symbol", "ensembl"), 
             genesetsize.min = 5, genesetsize.max = 1000)

Arguments

geneset.file

the file containing the gene set annotation.

geneIDs

gene IDs that have expression values in the studied data set.

geneID.type

indicating the type of gene IDs, gene symbol or emsembl gene IDs.

genesetsize.min

the minimum number of genes in a gene set that will be treated in the analysis.

genesetsize.max

the maximum number of genes in a gene set that will be treated in the analysis.

Details

TBA

Value

A SeqGeneSet object.

Author(s)

Xi Wang, xi.wang@newcastle.edu.au

See Also

newGeneSets, SeqGeneSet-class

Examples

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data(RCS_example, package="SeqGSEA")
geneIDs <- geneID(RCS_example)
geneID.type <- "ensembl"
geneset.file <- system.file("extdata", "gs_symb.txt",  package="SeqGSEA", mustWork=TRUE)
##
GS <- loadGenesets(geneset.file, geneIDs, geneID.type = geneID.type)
GS
## end 

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