HPEA {cinaR}

HPEA

Description

Hyper-geometric p-value enrichment analyses, looking for over-representation of a set of genes on given pathways.

Usage

HPEA(genes, geneset, background.genes.size)

Arguments

genes

DA gene names to be checked if they are over-represented or not.

geneset

Pathways to be used in enrichment analyses. If not set vp2008 (Chaussabel, 2008) immune modules will be used. This can be set to any geneset using 'read.gmt' function from 'qusage' package. Different modules are available: https://www.gsea-msigdb.org/gsea/downloads.jsp.

background.genes.size

number of background genes for hyper-geometric p-value calculations. Default is 20,000.

Value

data.frame, list of pathways and their enrichment (adjusted) p-values.

Examples

library(cinaR)

data("VP2008")
genes.to.test <- vp2008[[1]][1:10]
HPEA(genes.to.test,vp2008, background.genes.size = 20e3)