getPwmFromFile: generates a pwm from a file of different formats

In DiffLogo: DiffLogo: A comparative visualisation of biooligomer motifs

Description

Generates a pwm from a file of different formats. Supported formats are FASTA files (.fa, .fasta), alignment files (.txt, .text, .al, .alignment), PWM files (.pwm), JASPAR / Position Frequency Matrix files (.pfm), and homer files (.motif).

Usage

getPwmFromFile(filename)

Arguments

filename

the file

Value

a pwm

Examples

fileName = "extdata/pwm/H1-hESC.pwm"
file = system.file(fileName, package = "DiffLogo")
pwm = getPwmFromFile(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.