duplicates-methods: Retrieve numbers of duplicate reads.

In ChIPQC: Quality metrics for ChIPseq data

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))

ChIPQC documentation built on Nov. 8, 2020, 8:06 p.m.