trimPWMedge: Trim PWM edge

In MotIV: Motif Identification and Validation

Description

This function is use to cut edges with low information content.

Usage

  trimPWMedge(x, threshold=1)

Arguments

x	A matrix representing a PWM.
threshold	A transcription factor name or a list of TF names.

Value

A PWM.

Author(s)

Eloi Mercier <[e-mail]>

See Also

makePWM

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)

MotIV documentation built on April 28, 2020, 6:51 p.m.