enrichDiffLogoTableWithPvalues: Enriches a matrix of difflogo objects with p-values

In DiffLogo: DiffLogo: A comparative visualisation of biooligomer motifs

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)

Example output

Loading required package: cba
Loading required package: grid
Loading required package: proxy

Attaching package: ‘proxy’

The following objects are masked from ‘package:stats’:

    as.dist, dist

The following object is masked from ‘package:base’:

    as.matrix

[1] "pwm must be of class matrix or data.frame. Trying to convert"
[1] "pwm must be of class matrix or data.frame. Trying to convert"
[1] "pwm must be of class matrix or data.frame. Trying to convert"
[1] "pwm must be of class matrix or data.frame. Trying to convert"
[1] "pwm must be of class matrix or data.frame. Trying to convert"
[1] "pwm must be of class matrix or data.frame. Trying to convert"
[1] "pwm must be of class matrix or data.frame. Trying to convert"
[1] "pwm must be of class matrix or data.frame. Trying to convert"
[1] "pwm must be of class matrix or data.frame. Trying to convert"
[1] "pwm must be of class matrix or data.frame. Trying to convert"
[1] "pwm must be of class matrix or data.frame. Trying to convert"
[1] "pwm must be of class matrix or data.frame. Trying to convert"
[1] "pwm must be of class matrix or data.frame. Trying to convert"
[1] "pwm must be of class matrix or data.frame. Trying to convert"
[1] "pwm must be of class matrix or data.frame. Trying to convert"
[1] "pwm must be of class matrix or data.frame. Trying to convert"
[1] "pwm must be of class matrix or data.frame. Trying to convert"
[1] "pwm must be of class matrix or data.frame. Trying to convert"
[1] "pwm must be of class matrix or data.frame. Trying to convert"
[1] "pwm must be of class matrix or data.frame. Trying to convert"
[1] "pwm must be of class matrix or data.frame. Trying to convert"
[1] "pwm must be of class matrix or data.frame. Trying to convert"
[1] "pwm must be of class matrix or data.frame. Trying to convert"
[1] "pwm must be of class matrix or data.frame. Trying to convert"
[1] "pwm must be of class matrix or data.frame. Trying to convert"
[1] "pwm must be of class matrix or data.frame. Trying to convert"
[1] "pwm must be of class matrix or data.frame. Trying to convert"
[1] "pwm must be of class matrix or data.frame. Trying to convert"

DiffLogo documentation built on Nov. 8, 2020, 6:09 p.m.