outKegg2Gmt: outKegg2gmt

Description Usage Arguments Details Value Examples

View source: R/Run_pathwaysplice.R

Description

This function obtains a .gmt file for KEGG pathways.

Usage

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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

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## 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)

PathwaySplice documentation built on April 28, 2020, 7:44 p.m.