repicc: Calculating intraclass correlation coefficient using...

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

Calculating intraclass correlation coefficient using replicate samples

Description

The function can be used to calculate ICC for each CpG probe using balanced or unbalanced replicate samples.

Usage

repicc(dat,repid,mvalue=FALSE,nCores=2,qcflag=FALSE,qc=NULL,
       detPthre=0.05,nbthre=3)

Arguments

dat	Methylation beta value matrix
repid	A data frame with two variables, id and idx. id should be the same with column name of "dat", idx is a variable to show the relationship between samples with same value for samples from same individual.
mvalue	If TRUE, the beta value will be converted to M value for calculation of ICC
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

Value

A data frame containing ICC for each probe

Author(s)

Zongli Xu

References

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

Examples

if (require(minfiData)){
path <- file.path(find.package("minfiData"),"extdata")
rgSet <- readidat(path = path,recursive = TRUE)
mdat=getmeth(rgSet)
beta=getB(mdat,"Illumina")
repid=data.frame(id=c("5723646052_R02C02","5723646052_R04C01","5723646052_R05C02","5723646053_R04C02","5723646053_R05C02","5723646053_R06C02"),idx=c(1,2,3,1,2,3))
iccresu<-repicc(dat=beta,repid=repid)
}

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