EMA (version 1.4.3)

runHyperKEGG: Run KEGG pathway analysis based on hypergeometric test from a probeset list

Description

Run KEGG pathway analysis based on hypergeometric test from a probeset list

Usage

runHyperKEGG(list, pack.annot, categorySize = 1, name = "hyperKEGG",
htmlreport = TRUE, txtreport = TRUE, tabResult = FALSE, pvalue = 0.05)

Arguments

list

vector of character with probeset names

pack.annot

character string, annotation package to use

categorySize

integer, minimum size for category, by default = 1

name

character, name for output files, by default "hyperKEGG"

htmlreport

logical, if TRUE, a html report is created, by default TRUE

txtreport

logical, if TRUE, a txt report is created, by default TRUE

tabResult

logical, if TRUE, a list with the results is created, by default FALSE

pvalue

numeric, a cutoff for the hypergeometric test pvalue, by default 0.05

Value

• Txt and html report

  Data.frame with KEGG Id, pvalue, Odd Ratio, Expected count, Size and KEGG Term

Details

runHyperKEGG needs packages GOstats and KEGG.db from Bioconductor.

See Also

hyperGTest,runHyperGO

Examples

require(hgu133plus2.db)
data(marty)

## Probe list
probeList <- rownames(marty)[1:50]

## Hypergeometric test for KEGG pathway
res <- runHyperKEGG(probeList, htmlreport = FALSE, txtreport = FALSE,
    tabResult = TRUE, pack.annot = "hgu133plus2.db")