calcdetP: To calculate detection P values
In ENmix: Quality control and analysis tools for Illumina DNA methylation BeadChip

Description Usage Arguments Value Author(s) References Examples

Calculation of detection P values based on negtive internal control probes or out of the band (oob) probes

1	calcdetP(rgSet,detPtype = "negative")

`rgSet`	An object of class `rgDataSet`
`detPtype`	Calculation of detection P values based on negtive internal control ("negative") probes or out of the band ("oob") probes

An numerical matrix of detection P values, with row for CpGs and column for samples

Zongli Xu

Wanding Zhou et al. SeSAMe: reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions, Nucleic Acids Research, 2018

path <- file.path(find.package("minfiData"),"extdata")
rgSet <- readidat(path = path,recursive = TRUE)
detp=calcdetP(rgSet,detPtype = "negative")
detp2=calcdetP(rgSet,detPtype = "oob")