rcp: Illumina methylation array probe type bias correction
In ENmix: Quality control and analysis tools for Illumina DNA methylation BeadChip

Description Usage Arguments Details Value Author(s) References Examples

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

1 2	rcp(mdat, dist=25, quantile.grid=seq(0.001,0.999,by=0.001), qcscore = NULL, nbthre=3, detPthre=0.000001)

`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.

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.

A beta value matrix

Liang Niu, Zongli Xu

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

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)
}