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:

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

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

- padj – a BH-adjusted p-value;

- 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))

[Package fgsea version 1.16.0 Index]