getINCs: Extract intensity data for Illumina negative controls found...

In Oshlack/missMethyl: Analysing Illumina HumanMethylation BeadChip Data

Extract intensity data for Illumina negative controls found on 450k or EPIC arrays.

Description

Extracts the intensity data for the Illumina negative controls found on 450k or EPIC 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.

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 Type II probes for which the M-values are also given as the log2 ratio of the green to red intensities.

Value

An matrix of M-values.

Author(s)

Jovana Maksimovic

See Also

RGChannelSet

Examples

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

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

Oshlack/missMethyl documentation built on March 26, 2023, 1:50 p.m.