rnb.execute.normalization {RnBeads} | R Documentation

## 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`.

### Author(s)

Pavlo Lutsik

### 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")

[Package RnBeads version 1.12.1 Index]