rnb.execute.pOOBAH {RnBeads} | R Documentation

## rnb.execute.pOOBAH

### Description

Probe signal intensities are masked based on their out-of-band signal intensities to counter hybridization failure.

### Usage

    rnb.execute.pOOBAH(
      raw.set,
      anno.table = NULL,
      pval.thresh = 0.05,
      verbose = FALSE
    )

### Arguments

`raw.set` | Methylation dataset as an instance of `RnBeadRawSet`.
`anno.table` | Annotation for `raw.set`.
`pval.thresh` | Computed detection p-values above this threshold are masked. Default value is 0.05.
`verbose` | If set to true, a short information is printed on how many probes are masked by the method.

### Details

rnb.execute.pOOBAH is used to apply the method pOOBAH (P-value with OOB probes for Array Hybridization), which was conceived by Zhou, Triche, Laird and Shen to mask probes associated with hybridization failures. pOOBAH has been implemented in the R-package "sesame", a dependency needed for this function (see Zhou et al, 2018 and the respective Bioconductor/github pages). pOOBAH computes the detection p-values by constructing 2 empirical cumulative density functions (eCDFs) based on the out-of-band signal intensities of the red and the green channel, respectively, to detect hybridization failures. The (in-band) green and red channel signal intensities of the probes are passed to the eCDFs and the probes with a p-value higher than the given threshold (`pval.thresh`) are masked, as they are considered background. pOOBAH is applied separately to each sample. Hybridization failures might occur due to somatic or germline deletions. In addition, unreliable low-intensity probes might also be masked.

### Value

Returns a modified `RnBeadRawSet`, in which signal intensities are masked, if their computed p-value was greater than `pval.thresh`. Note, in datasets with several samples, signal intensities of a specific probe might be masked in sample A, but not in sample B, as pOOBAH is applied separately to each sample. For example: the signal intensities of probe cg24488772 might be masked in sample 1, but not in sample 12.

### Author(s)

pOOBAH method: Wanding Zhou. Adapted by Nathan Steenbuck.

### Examples

    library(RnBeads.hg19)
    data(small.example.object)
    filtered <- rnb.execute.pOOBAH(rnb.set.example)

[Package RnBeads version 2.12.2 Index]