enrichmentAnalysis: Perform pathway enrichment analysis on an ordered list of...

Description Usage Arguments Value

View source: R/ActivePathways.r

Description

Perform pathway enrichment analysis on an ordered list of genes

Usage

1
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


ActivePathways documentation built on July 10, 2020, 1:12 a.m.