lumiMethyB: Adjust background level of Illumina Infinium methylation data

In lumi: BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

Description

Adjust background level of Illumina Infinium methylation data, which is an object in MethyLumiM class.

Usage

lumiMethyB(methyLumiM, method = c("bgAdjust2C", "forcePositive", "none"), separateColor = FALSE, verbose = TRUE, overwriteBigMatrix=FALSE, ...)

Arguments

methyLumiM	a MethyLumiM object includes Illumina Infinium methylation data
method	background adjustment methods or user provided function, whose input and output should be a intensity matrix (pool of methylated and unmethylated probe intensities)
separateColor	determine whether to separately process two color channels
verbose	a boolean to decide whether to print out some messages
overwriteBigMatrix	whether to overwrite the result to the BigMatrix data, only valid when the input data is BigMatrix-based
...	other parameters used by corresponding method

Value

Return an object (same class as input methyLumiM) with updated "methylated" and "unmethylated" data matrix after background level adjustment.

Author(s)

Pan DU

See Also

See Also bgAdjustMethylation and estimateMethylationBG

Examples

data(example.lumiMethy)
lumiMethy.bgAdj = lumiB(example.lumiMethy)
attr(lumiMethy.bgAdj, "EstimatedBG")

lumi documentation built on Nov. 8, 2020, 5:27 p.m.