plotProfile: Plots a footprint estimated by Centipede

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 profile

Usage

plotProfile(Profile, Mlen = 0, xlab = "Dist. to motif (bp)", ylab =
"Cut-site probability", legTitle = "", legPos = "topright")

Arguments

Profile	A vector with the profile estimated by CENTIPEDE
Mlen	Length of the motif for drawing vertical lines delimiting it
xlab	Label of the x axis
ylab	Label for the y axis
legTitle	Title for one of the plot corners
legPos	Corner where to place the legTitle

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.