SolexaExportQA-class: (Legacy) Quality assessment summaries from Solexa export and...

In Bioconductor/ShortRead: FASTQ input and manipulation

(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 <[e-mail]>

See Also

qa.

Examples

showClass("SolexaExportQA")

Bioconductor/ShortRead documentation built on Nov. 2, 2024, 4:38 p.m.