reads-methods: Retrieve numbers of reads

In ChIPQC: Quality metrics for ChIPseq data

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))

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