computeGeneGSProb {CoGAPS}R Documentation

compute gene probability

Description

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.

Usage

computeGeneGSProb(object, GStoGenes, numPerm = 500, Pw = rep(1,
  ncol(object@featureLoadings)), PwNull = FALSE)

## S4 method for signature 'CogapsResult'
computeGeneGSProb(object, GStoGenes,
  numPerm = 500, Pw = rep(1, ncol(object@featureLoadings)),
  PwNull = FALSE)

Arguments

object

an object of type CogapsResult

GStoGenes

data.frame or list with gene sets

numPerm

number of permutations for null

Pw

weight on genes

PwNull

- logical indicating gene adjustment

Value

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


[Package CoGAPS version 3.6.0 Index]