loadGenesets {SeqGSEA} | R Documentation

## Load gene sets from files

### 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, xi.wang@newcastle.edu.au

### 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)

[Package SeqGSEA version 1.27.0 Index]