outKegg2Gmt: outKegg2gmt

In SCCC-BBC/PathwaySplice: An R Package for Unbiased Splicing Pathway Analysis in RNAseq data

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)

SCCC-BBC/PathwaySplice documentation built on May 9, 2019, 11:07 a.m.