bgAdjustMethylation: Estimate and adjust the background levels of Illumina Infinium methylaton microarrays

Description

Estimate and adjust the background levels of Illumina Infinium methylaton microarrays

Usage

bgAdjustMethylation(methyLumiM, separateColor = FALSE, targetBGLevel = 300, negPercTh = 0.25)

Arguments

methyLumiM

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

separateColor

determine whether separately process two color channels

targetBGLevel

adjust background level to a non-zero target background level

negPercTh

the threshold of the percentage of negative values after subtract estimated background levels. A warning will be given if too many probes having intensities lower than background levels.

Value

Return an object (same class as input methyLumiM) with updated "methylated" and "unmethylated" data matrix after background level adjustment. The estimated background level was kept in the attribute, "EstimatedBG", of the returned methyLumiM object.

Details

The estimation of background level of Infinium methylaton microarray is based on the assumption 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)
lumiMethy.bgAdj = bgAdjustMethylation(example.lumiMethy)
attr(lumiMethy.bgAdj, "EstimatedBG")