HyperGTestGeneEnrichment: Hyper Geometric Geneset Enrichement Test

In broadinstitute/ImagingAMARETTO: ImagingAMARETTO: tools for interpreting multi-omics networks for relevance to clinical outcomes and radiographic and histopathology imaging-derived biomarkers

Description

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

Usage

HyperGTestGeneEnrichment(gmtfile1, gmtfile2, runname1, runname2, NrCores,
  ref.numb.genes = 45956)

HyperGTestGeneEnrichment(gmtfile1, gmtfile2, runname1, runname2, NrCores,
  ref.numb.genes = 45956)

Arguments

gmtfile1	A gmtfilename that you want to compare
gmtfile2	A second gmtfile to compare with.
runname1	name of the first dataset.
runname2	name of the second dataset.
NrCores	Number of cores used for parallelization.
ref.numb.genes	The total number of genes teste, standard equal to 45 956 (MSIGDB standard).
gmtfile	The gmt file with reference gene set.
testgmtfile	The gmt file with gene sets to test. In our case, the gmt file of the modules.
NrCores	Number of cores for parallel computing.
ref.numb.genes	The reference number of genes.

Value

result

Creates resultfile with p-values and padj when comparing two gmt files with a hyper geometric test.

broadinstitute/ImagingAMARETTO documentation built on Dec. 3, 2019, 6:38 p.m.