prepareDiffLogoTable {DiffLogo} | R Documentation

## Prepare a table of difflogo objects

### Description

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

### Usage

    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

    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);

[Package DiffLogo version 2.12.2 Index]