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:

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]