imageCutSites: Plots and image with the cleavage pattern

In CENTIPEDE: CENTIPEDE learns a DNaseI footprint of a transcription factor and predicts its binding sites

Description

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

Usage

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

## 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 2, 2019, 6:50 p.m.