getPwmFromAlignment {DiffLogo} | R Documentation |
Creates a matrix-representation of a PWM from a set of sequences
getPwmFromAlignment(alignment, alphabet = NULL, pseudoCount = 0)
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 |
PWM as matrix
Hendrik Treutler
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)