readGademPWMFile: Read Gadem File

In alyst/MotIV: Motif Identification and Validation

Description

This function is use to read a gadem file containing PWM.

Usage

  readGademPWMFile(file)

Arguments

file	File's name.

Details

This function is made to read typicaly output file from Gadem (v1.2). Standard name is 'observedPWMs.txt'.

Author(s)

Eloi Mercier <[e-mail]>

Examples

#####Database and Scores#####
path <- system.file(package="MotIV")
jaspar <- readPWMfile(paste(path,"/extdata/jaspar2010.txt",sep=""))
jaspar.scores <- readDBScores(paste(path,"/extdata/jaspar2010_PCC_SWU.scores",sep=""))

#####Input#####
data(FOXA1_rGADEM)
motifs <- getPWM(gadem)
motifs.trimed <- lapply(motifs,trimPWMedge, threshold=1)

alyst/MotIV documentation built on May 12, 2019, 2:33 a.m.