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")