plotProfile: Plots a footprint estimated by Centipede

Description Usage Arguments Value References See Also Examples

View source: R/plotProfiles.R

Description

After fiting the CENTIPEDE model this function is useful for visualizing the footprint profile

Usage

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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

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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.