missMethyl (version 1.6.2)

getINCs: Extract intensity data for 613 Illumina negative controls found on 450k arrays.

Description

Extracts the intensity data for the 613 Illumina negative controls found on 450k arrays and returns a matrix of M-values (log2 ratio of the green to red intensities).

Usage

getINCs(rgSet)

Arguments

rgSet

An object of class RGChannelSet.

Value

• An matrix of M-values.

Details

The getINCs function extracts the intensity data for the INCs from an RGChannelSet object. The function retrieves both the green and red channel intensity values and returns the data as the log2 ratio of the green to red intensities. Essentially, the INCs are being treated like 450k Type II probes for which the M-values are also given as the log2 ratio of the green to red intensities.

See Also

RGChannelSet

Examples

if (require(minfi) & require(minfiData)) {

  INCs <- getINCs(RGsetEx)
  head(INCs)
  dim(INCs)
}