outKegg2Gmt {PathwaySplice} | R Documentation |
This function obtains a .gmt file for KEGG pathways.
outKegg2Gmt(organism.id, out.gmt.file)
organism.id |
an identifier for the organism being studied, for example, "hsa" for "Homo sapiens" |
out.gmt.file |
name of the output .gmt file |
The function calls the get.kegg.genesets
function in EnrichmentBrowser
R package
and modifies the resulting output into a .gmt file.
Returns a .gmt file for KEGG pathways
## 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)