MAQMapQA

MAQMapQA-class

report,MAQMapQA-method

report_html,MAQMapQA-method

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

classes

This package implements sampling, iteration, and input of
FASTQ files. The package includes functions for filtering and
trimming reads, and for generating a quality assessment report.
Data are represented as DNAStringSet-derived objects, and
easily manipulated for a diversity of purposes.  The package
also contains legacy support for early single-end, ungapped
alignment formats.

Bioconductor Package Maintainer

ShortRead

FASTQ input and manipulation

MAQMapQA-class function

Objects of the class are usually produced by a <code><a rd-options="" href="/link/qa?package=ShortRead&version=1.30.0" data-mini-rdoc="ShortRead::qa">qa</a></code>
 method.

Objects from the Class

<dl>
 <dt><code>.srlist</code>:</dt><dd>Object of class <code>"list"</code>, containing
 data frames or lists of data frames summarizing the results of
 qa.</dd> </dl>

Slots

Class <code>"SRList"</code>, directly.
Class <code>".QA"</code>, directly.
Class <code>".SRUtil"</code>, by class "SRList", distance 2.
Class <code>".ShortReadBase"</code>, by class ".QA", distance 2.

Extends

Accessor methods are inherited from the <code>SRList</code>
 class. 
 <dl>
 <dt>report</dt><dd><code>signature(x="MAQMapQA", ...,
 dest=tempfile(), type="html")</code>: produces an
 html file summarizing the QA results.</dd> </dl>

Methods

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

MAQMapQA-class: (Legacy) Quality assessment summaries from MAQ map files

Description

Arguments

Objects from the Class

Slots

Extends

Methods

See Also

Examples