calcGeneGSStat {CoGAPS}R Documentation

Probability Gene Belongs in Gene Set

Description

Probability Gene Belongs in Gene Set

Usage

calcGeneGSStat(Amean, Asd, GSGenes, numPerm, Pw = rep(1, ncol(Amean)),
  nullGenes = FALSE)

Arguments

Amean

A matrix mean values

Asd

A matrix standard deviations

GSGenes

data.frame or list with gene sets

numPerm

number of permutations for null

Pw

weight on genes

nullGenes

logical indicating gene adjustment

Details

calculates the probability that a gene listed in a gene set behaves like other genes in the set within the given data set

Value

gene similiarity statistic

Examples

data('SimpSim')
calcGeneGSStat(SimpSim.result$Amean, SimpSim.result$Asd, GSGenes=GSets[[1]],
numPerm=500)

[Package CoGAPS version 3.0.2 Index]