rnb.execute.quality

Description

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

Usage

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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

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