flagtagcounts-methods: Retrieve numbers of reads that pass various filters

In shengqh/ChIPQC: Quality metrics for ChIPseq data

Retrieve numbers of reads that pass various filters

Description

Retrieve numbers of reads that pass various filters

Methods

signature(object = "ChIPQCexperiment")

Retrieve a matrix of counts passing various filters for all the samples in an experiment. Each column represents the counts in a sample.

signature(object = "list")

Retrieve a matrix of counts passing various filters for all the samples in a list of ChIPQCsample objects. Each column represents the counts in a sample.

signature(object = "ChIPQCsample")

Retrieve a vector of counts passing various filters. The values are:

UnMapped	Number of reads that are not mapped (aligned)
Mapped	Number of reads that are mapped (aligned)
Duplicates	Number of reads that align to exactly the same place as another read
MapQPass	Number of reads with a mapping quality score greater than or equal to the specified threshold
MapQPassandDup	Number of reads that are mapped (aligned) and not duplicates

Author(s)

Thomas Carroll and Rory Stark

See Also

ChIPQC-package, ChIPQCexperiment, ChIPQCsample

Examples

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

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