rcp2: Modified RCP method

In xuz1/ENmix: Quality control and analysis tools for Illumina DNA methylation BeadChip

Modified RCP method

Description

Modified RCP method to normalize user's data to a list of reference values

Usage

        rcp2(datMeth, reference, quantile.grid=seq(0.001,0.999,by=0.001))

Arguments

datMeth	A matrix with row for probes and column for samples
reference	A data frame with two columns, "cg" for CpG names and "goldstandard" for reference values
quantile.grid	Quantile grid used in linear regression

Details

The function will normalize user data to a reference value distribution based on common set of probe between user data and reference data.

Value

A matrix with same dimension of user data

Author(s)

Zongli Xu

References

Liang Niu, Zongli Xu and Jack A. Taylor RCP: a novel probe design bias correction method for Illumina Methylation BeadChip, Bioinformatics 2016

Examples

require(minfiData)
path <- file.path(find.package("minfiData"),"extdata")
#based on rgDataset
rgSet <- readidat(path = path,recursive = TRUE)
meth=getmeth(rgSet)
beta=getB(meth)
reference=data.frame(cg=rownames(beta),goldstandard=beta[,3])
reference=reference[sample(1:nrow(reference),2000),]
beta2=rcp2(beta,reference)

xuz1/ENmix documentation built on Aug. 5, 2023, 7:11 a.m.