preprocess: Normalize a MethyLumiSet object using some popular choices

In skewr: Visualize Intensities Produced by Illumina's Human Methylation 450k BeadChip

Description

This is a wrapper function that allows normalizing of a MethyLumiSet using either a BeadStudio approximation, SWAN, or dasen. If desired, background correction only may be performed on the raw data.

Usage

preprocess(MethyLumiSet, norm = c("none", "illumina", "SWAN", "dasen"),
           bg.corr = TRUE)

Arguments

MethyLumiSet	A MethyLumiSet object
norm	The normalization method to be used
bg.corr	If TRUE, background subtarction using negative controls is performed. Ignored unless norm equals 'illumina' or 'none'

Details

Both Illumina style normalization via controls and the background correct method are handled by methylumi. The SWAN and dasen normalization methods are both performed by wateRmelon

Value

A MethyLumiSet

Author(s)

Ryan Putney [e-mail]

References

Davis S, Du P, Bilke S, Triche T, Jr. and Bootwalla M (2014). methylumi: Handle Illumina methylation data. R package version 2.12.0.

Maksimovic J, Gordon L, Oshlack A (2012). SWAN: Subset Quantile Within-Array Normalization for Illumina Infinium HumanMethylation450 BeadChips. Genome Biology, 13:R44.

Pidsley R, Wong CCY, Volta M, Lunnon K, Mill J, Schalwyk LC(2013). A data-driven approach to preprocessing Illumina 450k methylation array data. BMC Genomics, 14:293.

Schalkwyk LC, Pidsley R, Wong CC, Touleimat N, Defrance M, Teschendorff A and Maksimovic J (2013). wateRmelon: Illumina 450 methylation array normalization and metrics. R package version 1.5.1.

See Also

getMethyLumiSet

Examples

if(require('wateRmelon')) {
  data(melon)
  melon.dasen <- preprocess(melon, norm = 'dasen')
}

skewr documentation built on Nov. 8, 2020, 8:08 p.m.