list.to.go: GO term enrichment for a list of gene sets

In meghapadi/ALPACA:

Description

changed 3:57pm GO term enrichment is run using the GOstats package, and corrected for multiple testing using the Benjamini-Hochberg method.

Usage

list.to.go(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

list.to.go()

meghapadi/ALPACA documentation built on May 20, 2019, 6:47 p.m.