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]