RnBeads (version 1.4.0)

rnb.execute.normalization: rnb.execute.normalization

Description

Performs normalization of the provided HumanMethylation450 data set.

Usage

rnb.execute.normalization(object, method = rnb.getOption("normalization.method"), bgcorr.method = rnb.getOption("normalization.background.method"), verbose = TRUE)

Arguments

object

Methylation dataset as an object of type MethyLumiSet or RnBSet.

method

Normalization method, must be one of "none", "illumina", "swan", "minfi.funnorm", "bmiq", or wm.* where * stands for one of the methods implemented in wateRmelon package. Note that the execution of methods SWAN and minfi.funnorm requires packages minfi and IlluminaHumanMethylation450kmanifest. The BMIQ method requires the package RPMM. The wm.* methods naturally require wateRmelon.

bgcorr.method

Character singleton specifying which background subtraction should be used. Only methods impemented in the methylumi package are supported at the moment, namely methylumi.noob, methylumi.goob and methylumi.doob. See Triche et al. for detailed description of the methods.

verbose

flag specifying whether diagnostic output should be written to the console or to the RnBeads logger in case the latter is initialized

Value

Normalized dataset as an object of type RnBeadSet.

References

1. Triche, Timothy J., Jr., Weisenberger, Daniel J., Van Den Berg, David, Laird, Peter W. and Siegmund, Kimberly D. (2013) Low-level processing of Illumina Infinium DNA Methylation BeadArrays. Nucleic Acids Research 41(7):e90-e90.

Examples

library(RnBeads.hg19)
data(small.example.object)
logger.start(fname=NA)
rnb.set.norm<-rnb.execute.normalization(rnb.set.example, method="illumina", bgcorr.method="none")