imageCutSites: Plots and image with the cleavage pattern

Description Usage Arguments Value References See Also Examples

View source: R/imageCutSites.R

Description

After fiting the CENTIPEDE model this function is useful for visualizing the footprint cleavage pattern.

Usage

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imageCutSites(data, main="", xlab = "Dist. to motif (bp)")
imageCutSitesCombined(data, main="",xlab= "Dist. to motif (bp)",breaks)

Arguments

data

A matrix with the data supplied to CENTIPEDE

xlab

Label of the x axis

main

Title for the plot

breaks

Breaks for the color assigments

Value

No return value, just the plot

References

Roger Pique-Regi, Jacob F. Degner, Athma A. Pai, Daniel J. Gaffney, Yoav Gilad, Jonathan K. Pritchard. "Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data", Genome Research, Submitted Aug 2010

See Also

fitCentipede

Examples

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## Not run: 
#GETS EXAMPLE DATA FOR NRSF
data(NRSFcuts, package='CENTIPEDE')
data(NRSF_Anno, package='CENTIPEDE')

#FITS THE CENTIPEDE MODEL
centFit <- fitCentipede(Xlist = list(as.matrix(NRSFcuts)), Y=cbind(rep(1, dim(NRSF_Anno)[1]), NRSF_Anno[,5], NRSF_Anno[,6]))

#PLOTS IMAGE OF CUTSITES RANKED BY CENTIPEDE POSTERIORS
imageCutSites(NRSFcuts[order(centFit$PostPr),][c(1:100, (dim(NRSFcuts)[1]-100):(dim(NRSFcuts)[1])),])

#PLOT ESTIMATED FOOTPRINT
plotProfile(centFit$LambdaParList[[1]],Mlen=21)

## End(Not run)

CENTIPEDE documentation built on May 31, 2017, 5:05 a.m.