RnBeads (version 1.4.0)

rnb.execute.variability.removal: rnb.execute.variability.removal

Description

Removes all sites or probes with low variability from the given dataset.

Usage

rnb.execute.variability.removal(rnb.set, min.deviation = rnb.getOption("filtering.deviation.threshold"))

Arguments

rnb.set

Methylation dataset as an object of type inheriting RnBSet.

min.deviation

Threshold for standard deviation per site. This must be a scalar between 0 and 1. All sites, for which the standard deviation of methylation values (for all samples in rnb.set) is lower than this threshold, will be filtered out.

Value

List of four elements:

"dataset.before"

Copy of rnb.set.

"dataset"

The (possibly modified) dataset after removing sites with low variability.

"filtered"

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

"threshold"

The value of the given parameter min.deviation.

Examples

library(RnBeads.hg19)
data(small.example.object)
rnb.set.filtered <- rnb.execute.variability.removal(rnb.set.example, 0.01)