HGTGeneEnrichmentList: HGTGeneEnrichmentList Calculates the p-values for unranked...

In broadinstitute/CommunityAMARETTO: CommunityAMARETTO: A Computational Tool for the Discovery of Shared and Distinct Regulatory Mechanisms Across Biological Systems

Description

HGTGeneEnrichmentList

Calculates the p-values for unranked gene set enrichment based on two gmt files as input and the hyper geometric test.

Usage

HGTGeneEnrichmentList(genelist, gmtfile, NrCores, ref.numb.genes = 45956)

Arguments

genelist	The gmt file with reference gene set.
gmtfile	The gmt file with gene sets to test. In our case, the gmt file of the modules.
NrCores	Number of cores used for parallelization.
ref.numb.genes	The total number of genes teste, standard equal to 45956 (MSIGDB standard).

Value

a list a dataframe for Hypergeometric test

Examples

try(HGTGeneEnrichmentList(genelist,
  gmtfile,
  NrCores,
  ref.numb.genes = 45956))

broadinstitute/CommunityAMARETTO documentation built on April 6, 2020, 10:44 p.m.