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

Description Usage Arguments Value Examples

View source: R/fedup.R

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

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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

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# 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 15, 2021, 2:18 a.m.