computeGeneGSProb-methods: compute gene probability

In CoGAPS/CoGAPS: Coordinated Gene Activity in Pattern Sets

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.

CoGAPS/CoGAPS documentation built on June 23, 2024, 5:19 p.m.