Trim PWM edge

Description

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

Usage

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  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 <emercier@chibi.ubc.ca>

See Also

makePWM

Examples

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#####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)