loadGenesets: Load gene sets from files

In SeqGSEA: Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing

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

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

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.
singleCell	logical, whether to creat a SeqGeneSet object for scGSEA.

Details

TBA

Value

A SeqGeneSet object.

Author(s)

Xi Wang, [e-mail]

See Also

newGeneSets, SeqGeneSet-class

Examples

## Not run: 
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(Not run)

SeqGSEA documentation built on Nov. 8, 2020, 5:46 p.m.