View source: R/norm.quantile.R
norm.quantile | R Documentation |
Quantile normalization of methylation intensity data across samples for Illumina Infinium HumanMethylation 450 and MethylationEPIC BeadChip.
norm.quantile(mdat, method = "quantile1")
mdat |
An object of class |
method |
Quantile normalization method: "quantile1", "quantile2", or "quantile3". |
By default, method = "quantile1", which will separately quantile normalize Methylated or Unmethylated intensities for Infinium I or II probes. The "quantile2" will quantile normalize combined Methylated or Unmethylated intensities for Infinium I or II probes. The "quantile3" will quantile normalize combined Methylated or Unmethylated intensities for Infinium I and II probes together.
The output is an an object of class methDataSet
or MethylSet
.
Zongli Xu
Pidsley, R., CC, Y.W., Volta, M., Lunnon, K., Mill, J. and Schalkwyk, L.C. (2013) A data-driven approach to preprocessing Illumina 450K methylation array data. BMC genomics, 14, 293.
#for methDataSet
path <- file.path(find.package("minfiData"),"extdata")
rgSet <- readidat(path = path,recursive = TRUE)
mdat<-preprocessENmix(rgSet, bgParaEst="oob",nCores=6)
mdatq<-norm.quantile(mdat, method="quantile1")
#for MethySet
if (require(minfiData)) {
mdat=preprocessENmix(RGsetEx,bgParaEst="oob",nCores=6)
mdatq=norm.quantile(mdat,method="quantile1")
}
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