getPwmFromAlignment {DiffLogo} | R Documentation

## Create PWM from alignment

### Description

Creates a matrix-representation of a PWM from a set of sequences

### Usage

    getPwmFromAlignment(alignment, alphabet = NULL, pseudoCount = 0)

### Arguments

`alignment` | a vector or list of sequences each with equal length
`alphabet` | of type Alphabet
`pseudoCount` | the number of pseudo-observations for each character in the alphabet

### Value

PWM as matrix

### Author(s)

Hendrik Treutler

### Examples

    motif_folder= "extdata/alignments"
    motif_name = "calamodulin_1"
    fileName = paste(motif_folder,"/",motif_name,".txt",sep="")
    file = system.file(fileName, package = "DiffLogo")
    motif = getPwmFromAlignment(readLines(file), ASN, 1)
    seqLogo(pwm = motif, alphabet=ASN)

[Package DiffLogo version 2.14.0 Index]