rcp: Illumina methylation array probe type bias correction

Description Usage Arguments Details Value Author(s) References Examples

View source: R/rcp.R

Description

Probe design type bias correction using Regression on Correlated Probes (RCP) method

Usage

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        rcp(mdat, dist=25, quantile.grid=seq(0.001,0.999,by=0.001), qcscore = NULL,
 nbthre=3, detPthre=0.000001)

Arguments

mdat

An object of class methDataSet or MethylSet.

dist

Maximum distance in base pair between type I and type II probe pairs for regression calibration

quantile.grid

Quantile grid used in linear regression

qcscore

Data quality infomation object, the output from function QCinfo. If the object is provied, low quality data points as defined by detection p value threshold (detPthre) or number of bead threshold (nbthre) will be set as missing values.

detPthre

Detection P value threshold to define low qualitye data points

nbthre

Number of beads threshold to define low qualitye data points, nbthre=3 in default.

Details

The function will first identify type I and type II probe pairs within a specified distance, and then perform linear regression calibration between the probe types. With the estimates the function will then adjust type II data using type I data as references.

Value

A beta value matrix

Author(s)

Liang Niu, 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

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if (require(minfiData)) {
#methDataSet as input
path <- file.path(find.package("minfiData"),"extdata")
rgSet <- readidat(path = path,recursive = TRUE)
qc=QCinfo(rgSet)
mdat=preprocessENmix(rgSet,QCinfo=qc,nCores=6)
mdat=norm.quantile(mdat,method="quantile1")
beta=rcp(mdat)

#methylset as input
sheet <- read.metharray.sheet(file.path(find.package("minfiData"),"extdata"),
 pattern = "csv$")
rgSet <- read.metharray.exp(targets = sheet,extended = TRUE)
qc=QCinfo(rgSet)
mdat=preprocessENmix(rgSet,QCinfo=qc,nCores=6)
mdat=norm.quantile(mdat,method="quantile1")
beta=rcp(mdat)
}

ENmix documentation built on April 2, 2021, 6 p.m.