calcdetP {ENmix}R Documentation

To calculate detection P values

Description

Calculate 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

Calculate 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

## Not run: 
path <- file.path(find.package("minfiData"),"extdata")
rgSet <- readidat(path = path,recursive = TRUE)
detp=calcdetP(rgSet,detPtype = "negative")
detp2=calcdetP(rgSet,detPtype = "oob")

## End(Not run)

[Package ENmix version 1.25.1 Index]