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

In DChIPRep: DChIPRep - Analysis of chromatin modification ChIP-Seq data with replication

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

## S4 method for signature 'DChIPRepResults'
plotSignificance(object,
  meanFunction = robust_mean, 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)

DChIPRep documentation built on April 29, 2020, 4:26 a.m.