GMThyperGTest: Perform a Hypergeometric test, upon a GMT file. Much like...

Description Usage Arguments Value Author(s) See Also

View source: R/GSEAhyperGTest.R

Description

The type of identifier used doesn't matter much, as long as the same identifiers are used in genes and gmt, eg Gene Symbols.

Usage

1
GMThyperGTest(genes, gmt, adjust.method = "none")

Arguments

genes

a vector of gene symbols

gmt

a gmt object. see import.gsea.gmt

adjust.method

the multiple hypothesis correction value. see p.adjust. default=“none”

Value

a data.frame containing these columns: “GeneSet”, “x”, “m”, “n”, “k”, “Pval”, “FDR”, where:
“x” = the number of white balls drawn without replacement from an urn which contains both black and white balls.
“m” = the number of white balls in the urn.
“n” = the number of black balls in the urn.
“k” = the number of balls drawn from the urn.

Author(s)

Mark Cowley, 2009-01-15

See Also

phyper


drmjc/metaGSEA documentation built on Aug. 8, 2020, 1:53 p.m.