dupicc: Evaluation of measurement reliability using duplicate samples

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

Evaluation of measurement reliability using duplicate samples

Description

The function can be used to evaluate duplicate samples by calculating: 1) centered/un-centered Pearson's correlation coefficient between duplicates; 2) abosolute difference between duplicates; 3) ICC for each CpG probes using oneway or twoway model.

Usage

dupicc(dat,dupid,mvalue=FALSE,center=TRUE,nCores=2,qcflag=FALSE,qc=NULL,
       detPthre=0.05,nbthre=3,skipicc=FALSE,corfig=FALSE,model="oneway")

Arguments

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
model	Using "oneway" or "twoway" model to calculate ICC

Value

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.

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")
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)
}

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