BowtieQA-class {ShortRead} | R Documentation

## (Legacy) Quality assessment summaries from Bowtie files

### Description

This class contains a list-like structure with summary descriptions derived from visiting one or more Bowtie files.

### Objects from the Class

Objects of the class are usually produced by a `qa` method, with the argument `type="Bowtie"`.

### Slots

`.srlist`:

  Object of class `"list"`, containing data frames or lists of data frames summarizing the results of qa.

### Extends

Class `"SRList"`, directly. Class `".QA"`, directly. Class `".SRUtil"`, by class "SRList", distance 2. Class `".ShortReadBase"`, by class ".QA", distance 2.

### Methods

Accessor methods are inherited from the `SRList` class.

report

  `signature(x="BowtieQA", ..., dest=tempfile(), type="html")`: produces an html file summarizing the QA results.

### Author(s)

Martin Morgan <mtmorgan@fhcrc.org>

### See Also

`qa`.

### Examples

    showClass("BowtieQA")

[Package ShortRead version 1.42.0 Index]