lumiMethyB {lumi} | R Documentation |
Adjust background level of Illumina Infinium methylation data, which is an object in MethyLumiM class.
lumiMethyB(methyLumiM, method = c("bgAdjust2C", "forcePositive", "none"), separateColor = FALSE, verbose = TRUE, overwriteBigMatrix=FALSE, ...)
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 |
Return an object (same class as input methyLumiM) with updated "methylated" and "unmethylated" data matrix after background level adjustment.
Pan DU
See Also bgAdjustMethylation
and estimateMethylationBG
data(example.lumiMethy) lumiMethy.bgAdj = lumiB(example.lumiMethy) attr(lumiMethy.bgAdj, "EstimatedBG")