DChIPRep (version 1.2.3)

plotSignificance: Produce a plot that colors the positions identified as significant

Description

This function plots the positionwise mean of the two conditions after runTesting has been run on a DChIPRepResults object. The points corresponding to significant positions are colored black in both of the conditions. The function returns the plot as a ggplot2 object that can be modified afterwards.

Usage

"plotSignificance"(object, meanFunction = function(x) {     smhuber(x)$mu }, lfdrThresh = 0.2, ...)

Arguments

object

a DChIPRepResults object after runTesting

meanFunction

a function to compute the positionwise mean per group, defaults to a Huber estimator of the mean.

lfdrThresh

Threshold for the local FDR

...

additional parameters for plotting (NOT YET IMPLEMENTED)

Value

a ggplot2 object

Examples

data(testData)
dcr <- DChIPRepResults(testData)
dcr <- runTesting(dcr)
plotSignificance(dcr)