lumiMethyB: Adjust background level of Illumina Infinium methylation data

Description Usage Arguments Value Author(s) See Also Examples

View source: R/methylation_preprocessing.R

Description

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

Usage

1
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

1
2
3
data(example.lumiMethy)
lumiMethy.bgAdj = lumiB(example.lumiMethy)
attr(lumiMethy.bgAdj, "EstimatedBG")

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

Related to lumiMethyB in lumi...