fora {fgsea}R Documentation

Simple overrepresentation analysis based on hypergeometric test

Description

Simple overrepresentation analysis based on hypergeometric test

Usage

fora(pathways, genes, universe, minSize = 1, maxSize = Inf)

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:

Examples

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

[Package fgsea version 1.19.4 Index]