fora: Simple overrepresentation analysis based on hypergeometric...

In ctlab/fgsea: Fast Gene Set Enrichment Analysis

Simple overrepresentation analysis based on hypergeometric test

Description

Simple overrepresentation analysis based on hypergeometric test

Usage

fora(pathways, genes, universe, minSize = 1, maxSize = length(universe) - 1)

Arguments

pathways	List of gene sets to check.
genes	Set of query genes
universe	A universe from whiche 'genes' were selected
minSize	Minimal size of a gene set to test. All pathways below the threshold are excluded.
maxSize	Maximal size of a gene set to test. All pathways above the threshold are excluded.

Value

A table with ORA results. Each row corresponds to a tested pathway. The columns are the following:

• pathway – name of the pathway as in 'names(pathway)';

• pval – an enrichment p-value from hypergeometric test;

• padj – a BH-adjusted p-value;

• foldEnrichment – degree of enrichment relative to background;

• overlap – size of the overlap;

• size – size of the gene set;

• leadingEdge – vector with overlapping genes.

Examples

data(examplePathways)
data(exampleRanks)
foraRes <- fora(examplePathways, genes=tail(names(exampleRanks), 200), universe=names(exampleRanks))

ctlab/fgsea documentation built on Dec. 21, 2024, 1:55 p.m.