enrichDiffLogoTableWithPvalues {DiffLogo} | R Documentation

## Enriches a matrix of difflogo objects with p-values

### Description

Enriches a matrix of difflogo objects with p-values which quantifies the probability that two PWM-positions are from the same distribution

### Usage

    enrichDiffLogoTableWithPvalues(diffLogoObjMatrix, sampleSizes,
      stackHeight = shannonDivergence, numberOfPermutations = 100)

### Arguments

`diffLogoObjMatrix` | matrix of difflogo objects
`sampleSizes` | number of sequences behind the pwms behind the given difflogo objects
`stackHeight` | function for the calculation of a divergence measure for two probability vectors
`numberOfPermutations` | the number of permutations to perform for the calculation of stackHeights

### Value

matrix of difflogo objects enriched with p-values

### Author(s)

Martin Nettling

### Examples

    motif_folder= "extdata/pwm"
    motif_names = c("HepG2","MCF7","HUVEC","ProgFib")
    motifs = list()
    for (name in motif_names) {
      fileName = paste(motif_folder,"/",name,".pwm",sep="")
      file = system.file(fileName, package = "DiffLogo")
      motifs[[name]] = getPwmFromPwmFile(file)
    }
    sampleSizes <- c(100, 150, 200, 250)
    names(sampleSizes) <- motif_names

    diffLogoTableObj = prepareDiffLogoTable(motifs);
    diffLogoTableObj$diffLogoObjMatrix = enrichDiffLogoTableWithPvalues(diffLogoTableObj$diffLogoObjMatrix, sampleSizes)

[Package DiffLogo version 2.14.0 Index]