plotControlData: Plot the mean expression (with standard deviation bar) of different type of control probes

Description

Plot the mean intensity (with standard deviation bar) of different type of control probes. Multiple control types can be plotted in a single plot. The available control types can be get by running getControlType(controlData).

Usage

plotControlData(controlData, type = NULL, slideIndex = NULL, logMode = FALSE, new = TRUE, ...)

Arguments

controlData

a LumiBatch object including control data, a control data data.frame, a MethyLumiQC object or a MethyLumiM object including MethyLumiQC control data

type

the control probe type (case insensitive), which can be get by running getControlType(controlData)

slideIndex

the slide index or ID corresponding to each sample

logMode

whether show the data in log2 scale

new

whether refresh the new plot or add it on the old one

...

other parameters used by default plot function

Value

plot the picture and invisibly return TRUE if everything is OK

Details

When multiple control types are selected, they will be plotted in a two-column plot. For methylation data, the red and green channels will be plotted respectively in red and green colors.

Examples

Run this code

	controlFile <- system.file('doc', 'Control_Probe_Profile.txt', package='lumi')
	if (file.exists(controlFile)) {
	  	controlData <- getControlData(controlFile)
	    getControlType(controlData)
	    plotControlData(controlData, type='NEGATIVE')
	}