plotSignificance {DChIPRep} | R Documentation

## 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

    ## 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)

[Package DChIPRep version 1.16.0 Index]