getControlData: Get control probe information

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

Description

Get control probe information from Bead Studio output or a LumiBatch object.

Usage

getControlData(x, type = c('data.frame', 'LumiBatch'), ...)

Arguments

x	the control data can be a LumiBatch object or the Control Probe Profile file outputted by BeadStudio
type	determine the return data type
...	other parameters used by lumiR function

Value

By default, it returns a data.frame with first two columns as "controlType" and "ProbeID". The rest columns are the expression amplitudes for individual samples. When type is 'LumiBatch', it returns a LumiBatch object, which basically is the return of lumiR without combining duplicated TargetIDs. As the return is a LumiBatch object, it includes more information, like probe number, detection p-value and standard error of the measurement.

Author(s)

Pan Du

See Also

addControlData2lumi

Examples

	controlFile <- system.file('doc', 'Control_Probe_Profile.txt', package='lumi')
	if (file.exists(controlFile)) {
  	## return a data.frame
  	controlData <- getControlData(controlFile)
  	class(controlData)
  	names(controlData)

  	## return a LumiBatch object
  	controlData <- getControlData(controlFile, type='LumiBatch')
  	summary(controlData)
	}

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