calcGeneGSStat-methods: probability gene belongs in gene set

In CoGAPS: Coordinated Gene Activity in Pattern Sets

Description

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

Usage

calcGeneGSStat(
  object,
  GStoGenes,
  numPerm,
  Pw = rep(1, ncol(object@featureLoadings)),
  nullGenes = FALSE
)

## S4 method for signature 'CogapsResult'
calcGeneGSStat(
  object,
  GStoGenes,
  numPerm,
  Pw = rep(1, ncol(object@featureLoadings)),
  nullGenes = 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
nullGenes	logical indicating gene adjustment

Value

gene similiarity statistic

CoGAPS documentation built on Nov. 8, 2020, 5:02 p.m.