ChIPQC (version 1.8.2)

flagtagcounts-methods: 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 = "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

See Also

ChIPQC-package, ChIPQCexperiment, ChIPQCsample

Examples

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