flagtagcounts-methods {ChIPQC} | R Documentation

## 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))

[Package ChIPQC version 1.28.0 Index]