ActivePathways (version 1.0.1)

enrichmentAnalysis: Perform Gene Set Enrichment Analysis on an ordered list of genes

Description

Perform Gene Set Enrichment Analysis on an ordered list of genes

Usage

enrichmentAnalysis(genelist, gmt, background)

Arguments

genelist

character vector of gene names, in decreasing order of significance

gmt

GMT object

background

character vector of gene names. List of all genes being used as a statistical background

Value

a data.table of terms with the following columns:

term.id

The id of the term

term.name

The full name of the term

adjusted.p.val

The associated p-value adjusted for multiple testing

term.size

The number of genes annotated to the term

overlap

A character vector of the genes that overlap between the term and the query

Examples

# NOT RUN {
    enrichmentAnalysis(c('HERC2', 'SMC5', 'XPC', 'WRN'), gmt, makeBackground(gmt))
# }