ShortReadQA-class {ShortRead} | R Documentation

## Quality assessment of fastq files and ShortReadQ objects

### Description

These classes contains a list-like structure with summary descriptions derived from visiting one or more fastq files, or from a `ShortReadQ` object.

### Objects from the Class

Objects of the class are usually produced by a `qa` method.

### 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.

Additional methods defined on this class are:

report

  `signature(x="FastqQA", ..., dest=tempfile(), type="html")`: produces HTML files summarizing QA results. `dest` should be a directory.

report

  `signature(x="ShortReadQA", ..., dest=tempfile(), type="html")`: produces HTML files summarizing QA results. `dest` should be a directory.

### Author(s)

Martin Morgan <mtmorgan@fhcrc.org>

### See Also

`qa`.

### Examples

    showClass("FastqQA")

[Package ShortRead version 1.42.0 Index]