getPwmFromFastaFile: generates a pwm from a FASTA file

In DiffLogo: DiffLogo: A comparative visualisation of biooligomer motifs

Description

generates a pwm from a FASTA file

Usage

getPwmFromFastaFile(filename, alphabet = NULL)

Arguments

filename	the FASTA file
alphabet	the desired alphabet of type Alphabet

Value

a pwm

Examples

fileName = "extdata/alignments/F-box_bacteria.seq.fa"
file = system.file(fileName, package = "DiffLogo")
pwm = getPwmFromFastaFile(file)

Example output

Loading required package: cba
Loading required package: grid
Loading required package: proxy

Attaching package: ‘proxy’

The following objects are masked from ‘package:stats’:

    as.dist, dist

The following object is masked from ‘package:base’:

    as.matrix

DiffLogo documentation built on Nov. 8, 2020, 6:09 p.m.