SolexaExportQA-class {ShortRead} | R Documentation

## (Legacy) Quality assessment summaries from Solexa export and realign files

### Description

This class contains a list-like structure with summary descriptions derived from visiting one or more Solexa ‘export’ or ‘realign’ files.

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

report

  `signature(x="SolexaExportQA", ..., dest=tempfile(), type="pdf")`: (deprecated; use `type="html"` instead) produces a pdf file summarizing QA results. `dest` should be a file.

report

  `signature(x="SolexaRealignQA", ..., 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("SolexaExportQA")

[Package ShortRead version 1.36.1 Index]