rnb.execute.na.removal: rnb.execute.na.removal

In RnBeads: RnBeads

Description

Removes all probes with missing value (if such exists) from the given dataset.

Usage

rnb.execute.na.removal(
  rnb.set,
  threshold = rnb.getOption("filtering.missing.value.quantile")
)

Arguments

rnb.set	Methylation dataset as an object of type inheriting RnBSet.
threshold	Maximum quantile of NAs allowed per site. This must be a value between 0 and 1.

Value

List of four or five elements:

"dataset.before"

Copy of rnb.set.

"dataset"

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

"filtered"

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

"threshold"

Copy of threshold.

"naCounts"

Vector storing the number of NAs per site

Author(s)

Yassen Assenov

Examples

library(RnBeads.hg19)
data(small.example.object)
rnb.set.filtered <- rnb.execute.na.removal(rnb.set.example, 0)$dataset
identical(meth(rnb.set.example), meth(rnb.set.filtered)) # TRUE

RnBeads documentation built on March 3, 2021, 2 a.m.