rnb.execute.snp.removal {RnBeads} | R Documentation

## rnb.execute.snp.removal

### Description

Removes all probes overlapping with single nucleotide polymorphisms (SNPs) from the given dataset.

### Usage

    rnb.execute.snp.removal(rnb.set, snp = rnb.getOption("filtering.snp"))

### Arguments

`rnb.set` | Methylation dataset as an object of type inheriting `RnBSet`.
`snp` | Criterion for the removal of sites or probes based on overlap with SNPs. Possible values are `"no"`, `"3"`, `"5"`, `"any"` or `"yes"`. See the documentation of `rnb.options` for a detailed explanation of the procedures these values encode.

### Value

`list` of four elements:

`"dataset.before"`

  Copy of `rnb.set`.

`"dataset"`

  The (possibly) modified dataset object after removing probes that overlap with SNPs.

`"filtered"`

  `integer` vector storing the indices (in beta matrix of the unfiltered dataset) of all removed sites or probes.

`"snp"`

  The value of the `snp` parameter.

### Author(s)

Yassen Assenov

### Examples

    library(RnBeads.hg19)
    data(small.example.object)
    rnb.set.filtered <- rnb.execute.snp.removal(rnb.set.example, "any")$dataset
    identical(meth(rnb.set.example), meth(rnb.set.filtered)) # FALSE

[Package RnBeads version 2.2.0 Index]