plotControlData: Plot the mean expression (with standard deviation bar) of...

In lumi: BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

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

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.

Value

plot the picture and invisibly return TRUE if everything is OK

Author(s)

Pan Du

See Also

addControlData2lumi and addControlData2methyLumiM

Examples

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

lumi documentation built on Nov. 8, 2020, 5:27 p.m.