rnb.execute.na.removal

Share:

Description

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

Usage

1
2
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

1
2
3
4
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

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.