prepareDiffLogoTable: Prepare a table of difflogo objects

Description Usage Arguments Value Author(s) Examples

Description

Prepares a DiffLogoTable and generates an object that contains the hirarchical clustering and a matrix of prepared difference logos.

Usage

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prepareDiffLogoTable(PWMs, alphabet = DNA, configuration = list())

Arguments

PWMs

a list/vector of position weight matrices (PWMs) each of type pwm, data.frame, or matrix

alphabet

the alphabet of the given PWMs

configuration

list of (probably part of) of configuration options. See diffLogoTableConfiguration.

Value

matrix of difference logos

Author(s)

Martin Nettling

Examples

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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)

diffLogoTableObj = prepareDiffLogoTable(motifs);

mgledi/DiffLogo documentation built on June 7, 2020, 8:23 a.m.