duplicates-methods {ChIPQC} | R Documentation

## Retrieve numbers of duplicate reads.

### Description

Retrieve the numbers of duplicate reads.

### Methods

`signature(object = "ChIPQCexperiment", bFiltered)`

  Retrieve a `vector` of the numbers of duplicate reads for each sample in an experiment. A read is considered duplicated if another read maps to the same genomic location. If `bFiltered=TRUE` (or is missing), this will be the number of duplicates that pass the mapping quality filter for each sample. if `bFiltered=FALSE`, it will be the total number of duplicates for each sample.

`signature(object = "list", bFiltered)`

  Retrieve a `vector` of the numbers of duplicate reads for each sample in a list of ChIPQCsample objects. A read is considered duplicated if another read maps to the same genomic location. If `bFiltered=TRUE` (or is missing), this will be the number of duplicates that pass the mapping quality filter for each sample. if `bFiltered=FALSE`, it will be the total number of duplicates for each sample.

`signature(object = "ChIPQCsample", bFiltered)`

  Retrieve the number of duplicates for a sample. A read is considered duplicated if another read maps to the same genomic location. If `bFiltered=TRUE` (or is missing), this will be the number of duplicates that pass the mapping quality filter. if `bFiltered=FALSE`, it will be the total number of duplicates for the sample.

### Author(s)

Thomas Carroll and Rory Stark

### See Also

ChIPQC-package, ChIPQCexperiment, ChIPQCsample

### Examples

    data(example_QCexperiment)
    duplicates(exampleExp)
    duplicates(QCsample(exampleExp,1))

[Package ChIPQC version 1.23.1 Index]