calcdetP: To calculate detection P values

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

To calculate detection P values

Description

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

Usage

calcdetP(rgSet,detPtype = "negative")

Arguments

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

Value

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

Author(s)

Zongli Xu

References

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

Examples

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

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