lumiMethyC: Color bias adjust of Illumina Infinium methylation data

Description

Color bias adjust of Illumina Infinium methylation data, which is an object in MethyLumiM class.

Usage

lumiMethyC(methyLumiM, method = c("quantile", "ssn", "none"), verbose = TRUE, overwriteBigMatrix=FALSE, ...)

Arguments

methyLumiM

a MethyLumiM object includes Illumina Infinium methylation data

method

color bias adjustment methods or user provided function, see "details" for more information of user defined function.

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.

Details

The first two arguments of the user defined function should be two intensity matrix (pool of methylated and unmethylated probe intensities) of red and green channel respectively. The return of the user defined function should be a list including color adjusted matrix of red and green channel. For example: return(list(red=redData, green=grnData)). "redData" and "grnData" are two color adjusted matrix.

Examples

Run this code

data(example.lumiMethy)
# before adjustment
plotColorBias1D(example.lumiMethy)
# plot in 2D plot of one selected sample
plotColorBias2D(example.lumiMethy, selSample = 1)
lumiMethy.adj = lumiMethyC(example.lumiMethy)
# after adjustment
plotColorBias1D(lumiMethy.adj)
# plot in 2D plot of one selected sample
plotColorBias2D(lumiMethy.adj, selSample = 1)