runFedup {fedup} | R Documentation

## Runs pathway enrichment and depletion analysis using a Fisher's exact test.

### Description

This function takes a list of test genes and a common background set to calculate enrichment and depletion for a list of pathways. The method allows for fast and efficient testing of multiple gene sets of interest.

### Usage

    runFedup(genes, pathways)

### Arguments

`genes` | (list) named list of vectors with background genes and `n` test genes.
`pathways` | (list) named list of vectors with pathway annotations.

### Value

List of length `n` with table(s) of pathway enrichment and depletion results. Rows represent tested pathways. Columns represent:

- pathway – name of the pathway, corresponds to names(`pathways`);

- size – size of the pathway;

- real_frac – fraction of test gene members in pathway;

- expected_frac – fraction of background gene members in pathway;

- fold_enrichment – fold enrichment measure, evaluates as `real_frac` / `expected_frac`;

- status – indicator that pathway is enriched or depleted for test gene members;

- real_gene – vector of test gene members annotated to `pathways`;

- pvalue – enrichment p-value calculated via Fisher's exact test;

- qvalue – BH-adjusted p-value

### Examples

    # Load pathway annotations
    data(pathwaysGMT)
    # Run fedup with a single test set
    data(geneSingle)
    fedupRes <- runFedup(geneSingle, pathwaysGMT)
    # Run fedup with two test sets
    data(geneDouble)
    fedupRes <- runFedup(geneDouble, pathwaysGMT)
    # Run fedup with multiple test sets
    data(geneMulti)
    fedupRes <- runFedup(geneMulti, pathwaysGMT)

[Package fedup version 1.2.0 Index]