runFedup: Runs pathway enrichment and depletion analysis using a...

In rosscm/fedup: Fisher's Test for Enrichment and Depletion of User-Defined Pathways

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)

rosscm/fedup documentation built on July 19, 2021, 2:21 a.m.