getPwmFromAlignment: Create PWM from alignment

Description Usage Arguments Value Author(s) Examples

View source: R/utilities.R

Description

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

Usage

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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

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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)
(pwm = motif, alphabet=ASN)

DiffLogo documentation built on Nov. 1, 2018, 2:24 a.m.