rnb.execute.quality: rnb.execute.quality

In RnBeads: RnBeads

Description

Performs quality control calculations on the loaded DNA methylation data set.

Usage

rnb.execute.quality(
  object,
  type = "sites",
  qc.coverage.plots = rnb.getOption("qc.coverage.plots"),
  verbose = TRUE
)

Arguments

object	Methylation dataset as an object of class RnBeadSet, RnBeadRawSet or RnBiseqSet.
type	character vector of length 1 giving the type of genomic regions for which the quality control information is summarized.
qc.coverage.plots	Flag indicating if sequencing coverage information is summarized and returned. This parameter is considered only when object is of type RnBiseqSet.
verbose	Flag specifying whether diagnostic output should be written to the console or to the RnBeads logger in case the latter is initialized.

Details

Currently, summarizing coverage for RnBiseqSet object is the only available function.

Value

RnBeadSet object with imputed quality control information

Author(s)

Pavlo Lutsik

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