dupicc: Evaluation of measurement reliability using duplicate samples
In ENmix: Quality control and analysis tools for Illumina DNA methylation BeadChip

Description Usage Arguments Value Author(s) References Examples

The function can be used to calculate ICC for each CpG probe, and/or centered/un-centered Pearson's correlation coefficient between duplicate samples.

1 2	dupicc(dat,dupid,mvalue=FALSE,center=FALSE,nCores=2,qcflag=FALSE,qc=NULL, detPthre=0.05,nbthre=3,skipicc=FALSE,corfig=FALSE,...)

`dat`	Methylation beta value matrix
`dupid`	A data frame with two variables, id1 and id2. The two ids in each row indicate a duplicate pair. These ids should be the same with column names of the input methylation matrix
`mvalue`	If TRUE, the beta value will be converted to M value for calculation of ICC
`center`	If TRUE, the methylation beta values will be centered for each CpG before calculation of ICC or correlation
`nCores`	Number of cores will be used for calculation of ICC
`qcflag`	Whether to perform QC before calculation of ICC
`qc`	QC object from function QCinfo
`detPthre`	If qcflag=TRUE, the methylation values with detection P value higher than the threshold will be removed before calculation
`nbthre`	If qcflag=TRUE, the methylation values with number of bead smaller than the threshold will be removed
`skipicc`	If TRUE, ICC calculation will be skipped
`corfig`	If TRUE, a figure will be generated to demonstrate correlations within duplicates or within non-duplicates
`...`	Any further arguments for function "icc" in R package "irr"

icc: a data frame containing ICC and P values for each probe

dupcor: a data frame containing Pearson's correlation and averaged absolute difference between duplicates.

Zongli Xu

Zongli Xu, Jack A Taylor. Reliability of DNA methylation measures using Illumina methylation BeadChip. Epigenetics 2020

if (require(minfiData)){
path <- file.path(find.package("minfiData"),"extdata")
rgSet <- readidat(path = path,recursive = TRUE)
mdat=getmeth(rgSet)
beta=getB(mdat,"Illumina")
dupidx=data.frame(id1=c("5723646052_R02C02","5723646052_R04C01","5723646052_R05C02"),
id2=c("5723646053_R04C02","5723646053_R05C02","5723646053_R06C02"))
iccresu<-dupicc(dat=beta,dupid=dupidx)
}