calcdetP {ENmix} | R Documentation

## 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")

[Package ENmix version 1.28.8 Index]