duplicateRate-methods: Retrieve duplication rates

In shengqh/ChIPQC: Quality metrics for ChIPseq data

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))

shengqh/ChIPQC documentation built on Feb. 27, 2023, 10:51 p.m.