RnBeads (version 1.4.0)

rnb.execute.snp.removal: 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.

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