dupicc {ENmix} | R Documentation |
Calcuate ICC (consistency and twoway) and Pearson's correlation coefficient for each CpG probes. Calculate Pearson's correlation coefficient and methylation differences between duplicate samples.
dupicc(dat,dupid,mvalue=FALSE,center=FALSE,ncores=2,qcflag=FALSE,qc=NULL,detPthre=0.05,nbthre=3)
dat |
Methylation beta value matrix |
dupid |
A data frame with two variables, id1 and id2, for corresponding duplicates ids in methylation matrix |
mvalue |
Whether to convert to M value for calculation of ICC |
center |
Whether methylation beta values will be centered for calculation of correlation between duplicate samples |
ncores |
Number of core will be used for calculation of ICC |
qcflag |
Whether to perform QC before calculation of ICC |
qc |
QC object from ENmix package |
detPthre |
Detection P value threshold to identify low quality data point |
nbthre |
Number of bead threshold to identify low quality data point |
icc: a data frame contain ICC and P values for each probes
dupcor: a data frame contain Pearson's correlation and averaged absolute difference between duplicates.
Zongli Xu
Zongli Xu, Liang Niu, Leping Li and Jack A. Taylor, ENmix: a novel background correction method for Illumina HumanMethylation450 BeadChip. Nucleic Acids Research 2015.
if(FALSE){ if (require(minfiData)) { sheet <- read.metharray.sheet(file.path(find.package("minfiData"),"extdata"), pattern = "csv$") rgSet <- read.metharray.exp(targets = sheet,extended = TRUE) mdat=preprocessRaw(rgSet) beta=getBeta(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) }}