getControlData {lumi}R Documentation

Get control probe information

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')
        ## return a data.frame
        controlData <- getControlData(controlFile)
        class(controlData)
        names(controlData)
        
        ## return a LumiBatch object
        controlData <- getControlData(controlFile, type='LumiBatch')
        summary(controlData)

[Package lumi version 1.8.3 Index]