getPwmFromAlignment: Create PWM from alignment

In mgledi/DiffLogo: DiffLogo: A comparative visualisation of biooligomer motifs

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)

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