alpacaListToGo: GO term enrichment for a list of gene sets

In netZoo/netZooR: Unified methods for the inference and analysis of gene regulatory networks

GO term enrichment for a list of gene sets

Description

GO term enrichment is run using the GOstats package, and corrected for multiple testing using the Benjamini-Hochberg method.

Usage

alpacaListToGo(gene.list, univ.vec, comm.nums)

Arguments

gene.list	A list consisting of vectors of genes; genes must be identified by their official gene symbols.
univ.vec	A vector of all gene symbols that were present in the original network. This set is used as the universe for running the hypergeometric test in GOstats.
comm.nums	A vector of names for the gene sets in the input parameter "gene.list". These are used to create the table of final results.

Value

A table whose rows represent enriched GO terms (p_adj<0.05) and columns describe useful properties, like the name of the GO term, the label of the gene set which is enriched in that GO term, the adjusted p-value and Odds Ratio.

Examples

a <- 1 # example place holder

netZoo/netZooR documentation built on Oct. 16, 2024, 10:23 p.m.