calc_detP {ENmix} | R Documentation

## Calculate detection P values

### Description

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

### Usage

    calc_detP(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. eSAMe: 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=calc_detP(rgSet,detPtype = "negative")
    detp2=calc_detP(rgSet,detPtype = "oob")

    ## End(Not run)

[Package ENmix version 1.23.5 Index]