cinaR (version 0.2.3)

HPEA: 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

# NOT RUN {
library(cinaR)

data("VP2008")
genes.to.test <- vp2008[[1]][1:10]
HPEA(genes.to.test,vp2008, background.genes.size = 20e3)
# }
# NOT RUN {
# }