estimateMethylationBG: Estimate the background levels of Illumina Infinium methylaton microarrays

Description

Estimate the background levels of Illumina Infinium methylaton microarrays. It is called by function bgAdjustMethylation

Usage

estimateMethylationBG(methyLumiM, separateColor = FALSE, nbin = 1000)

Arguments

methyLumiM

a MethyLumiM object or any eSet object with "methylated" and "unmethylated" data matrix element in the assayData slot

separateColor

determine whether to separately process two color channels

nbin

the number of bins in the histogram used to estimate the mode position of the density

Value

a vector of estimated background levels for individual samples.

Details

When the controlData includes the negative control probe information, the background estimation will be the median of the negative control probes. Red and Green color channels will be estimated separately.

In the case the negative control data is not available, the background will be estimated based on the mode positions of unmethylated or methylated distribution (the smaller one). The assumption is that the lots of CpG sites are unmethylated, which results in a density mode of the intensities measured by methylated probes. The position of this mode represents the background level.

Examples

Run this code

data(example.lumiMethy)
estimatedBG = estimateMethylationBG(example.lumiMethy)
estimatedBG