computeGeneGSProb {CoGAPS}R Documentation

Compute Gene Probability

Description

Compute Gene Probability

Usage

computeGeneGSProb(Amean, Asd, GSGenes, Pw = rep(1, ncol(Amean)),
  numPerm = 500, PwNull = FALSE)

Arguments

Amean

A matrix mean values

Asd

A matrix standard deviations

GSGenes

data.frame or list with gene sets

Pw

weight on genes

numPerm

number of permutations for null

PwNull

- logical indicating gene adjustment

Details

Computes the p-value for gene set membership using the CoGAPS-based statistics developed in Fertig et al. (2012). This statistic refines set membership for each candidate gene in a set specified in GSGenes by comparing the inferred activity of that gene to the average activity of the set.

Value

A vector of length GSGenes containing the p-values of set membership for each gene containined in the set specified in GSGenes.

Examples

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

[Package CoGAPS version 3.0.2 Index]