enrichDiffLogoObjectWithPvalues {DiffLogo} | R Documentation

## Enriches a difflogo object with p-values

### Description

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

### Usage

    enrichDiffLogoObjectWithPvalues(diffLogoObj, n1, n2,
      stackHeight = shannonDivergence, numberOfPermutations = 100)

### Arguments

`diffLogoObj` | matrix of difflogo objects
`n1` | the number of sequences behind the first pwm behind the given difflogo object
`n2` | the number of sequences behind the second pwm behind the given difflogo object
`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

enriched difflogo object

### 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)
    }

    pwm1 = motifs[[motif_names[[1]]]]
    pwm2 = motifs[[motif_names[[2]]]]
    n1 <- 100
    n2 <- 100
    diffLogoObj = createDiffLogoObject(pwm1 = pwm1, pwm2 = pwm2)
    diffLogoObj = enrichDiffLogoObjectWithPvalues(diffLogoObj, n1, n2)

[Package DiffLogo version 2.4.0 Index]