duplicateRate-methods {ChIPQC} | R Documentation

## Retrieve duplication rates

### Description

Retrieve duplication rates.

### Methods

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

  Retrieve a `vector` of the duplication rates for each sample in an experiment. A read is considered duplicated if another read maps to the same genomic location; the duplication rate is the number of duplicated reads divided by the total number of reads for a sample. If `bFiltered=TRUE` (or is missing), only reads that pass the mapping quality filter for each sample are included. if `bFiltered=FALSE`, all reads for each sample will be included.

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

  Retrieve a `vector` of the duplication rates for each sample in a list of ChIPQCsample objects. A read is considered duplicated if another read maps to the same genomic location; the duplication rate is the number of duplicated reads divided by the total number of reads for a sample. If `bFiltered=TRUE` (or is missing), only reads that pass the mapping quality filter for each sample are included. if `bFiltered=FALSE`, all reads for each sample will be included.

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

  Retrieve the duplication rate for a sample. A read is considered duplicated if another read maps to the same genomic location; the duplication rate is the number of duplicated reads divided by the total number of reads for the sample. If `bFiltered=TRUE` (or is missing), only reads that pass the mapping quality filter for the sample are included. if `bFiltered=FALSE`, all reads for the sample will be included.

### Author(s)

Thomas Carroll and Rory Stark

### See Also

ChIPQC-package, ChIPQCexperiment, ChIPQCsample

### Examples

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

[Package ChIPQC version 1.16.1 Index]