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

In ActivePathways: Integrative Pathway Enrichment Analysis of Multivariate Omics Data

Perform pathway enrichment analysis on an ordered list of genes

Description

Perform pathway 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

ActivePathways documentation built on Sept. 11, 2024, 8:45 p.m.