RnBeads (version 1.4.0)

rnb.execute.context.removal: rnb.execute.context.removal

Description

Removes all probes that belong to specific context from the given dataset.

Usage

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

Arguments

rnb.set

Methylation dataset as an object of type RnBeadSet.

contexts

Probe contexts to be filtered out.

Value

List of three or four elements:

"dataset.before"

Copy of rnb.set.

"dataset"

The (possibly modified) RnBeadSet object after performing the missing value removal.

"filtered"

integer vector storing the indices of all removed probes in dataset.before.

"contexts"

The value of the parameter contexts.

Examples

library(RnBeads.hg19)
data(small.example.object)
contexts.to.ignore <- c("CC", "CAG", "CAH")
rnb.set.filtered <- rnb.execute.context.removal(rnb.set.example, contexts.to.ignore)$dataset
identical(rnb.set.example, rnb.set.filtered) # FALSE