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 3.10.0 Index]