reads-methods: Retrieve numbers of reads

In shengqh/ChIPQC: Quality metrics for ChIPseq data

Retrieve numbers of reads

Description

Retrieve the numbers of reads.

Methods

signature(object = "ChIPQCexperiment", bFiltered)

Retrieve a vector of the numbers of reads for each sample in an experiment. If bFiltered=TRUE (or is missing), this will be the number of reads that pass the mapping quality filter for each sample. if bFiltered=FALSE, it will be the total number of reads for each sample.

signature(object = "list", bFiltered)

Retrieve a vector of the numbers of reads for each sample in a list of ChIPQCsample objects. If bFiltered=TRUE (or is missing), this will be the number of reads that pass the mapping quality filter for each sample. if bFiltered=FALSE, it will be the total number of reads for each sample.

signature(object = "ChIPQCsample", bFiltered)

Retrieve the number of reads for a sample. If bFiltered=TRUE (or is missing), this will be the number of reads that pass the mapping quality filter. if bFiltered=FALSE, it will be the total number of reads for the sample.

Author(s)

Thomas Carroll and Rory Stark

See Also

ChIPQC-package, ChIPQCexperiment, ChIPQCsample

Examples

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

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