plotControlData {lumi} | R Documentation

## 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

### 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')
    	}

[Package lumi version 2.44.0 Index]