outKegg2Gmt {PathwaySplice} | R Documentation

## outKegg2gmt

### Description

This function obtains a .gmt file for KEGG pathways.

### Usage

    outKegg2Gmt(organism.id, out.gmt.file)

### Arguments

`organism.id` | an identifier for the organism being studied, for example, "hsa" for "Homo sapiens"
`out.gmt.file` | name of the output .gmt file

### Details

The function calls the `get.kegg.genesets` function in `EnrichmentBrowser` R package and modifies the resulting output into a .gmt file.

### Value

Returns a .gmt file for KEGG pathways

### Examples

    ## Not run:

    data.dir <-  tempdir()
    outKegg2Gmt ("hsa",file.path(data.dir,"kegg.gmt.txt"))

    kegg.pathways <- gmtGene2Cat(file.path(data.dir, "kegg.gmt.txt"),genomeID = "hg19")

    result.kegg <- runPathwaySplice(genewise.table = gene.based.table.fdr,
                                   genome = "hg19",
                                   id = "ensGene",
                                   gene2cat = kegg.pathways,
                                   go.size.limit = c(5, 100),
                                   method = "Wallenius",
                                   use.genes.without.cat = TRUE)

    ## End(Not run)

[Package PathwaySplice version 1.10.0 Index]