QA-class: (Updated) classes for representing quality assessment results

In Bioconductor/ShortRead: FASTQ input and manipulation

(Updated) classes for representing quality assessment results

Description

Classes derived from .QA-class represent results of quality assurance analyses.

Objects from the Class

Users create instances of many of these classes by calling the corresponding constructors, as documented on the help page for qa2. Classes constructed in this way include QACollate, QAFastqSource, QAAdapterContamination, QAFrequentSequence, QANucleotideByCycle, QANucleotideUse, QAQualityByCycle, QAQualityUse, QAReadQuality, and QASequenceUse.

The classes QASource, QAFiltered, QAFlagged and QASummary are generated internally, not by users.

Extends

.QA2 extends class ".ShortReadBase", directly.

QASummary is a virtual class extending .QA2; all user-creatable classes extend QASummary.

QASource extends QASummary. All classes used to represent raw data input (QAFastqSource) extend QASource.

QAData is a reference class, used to contain a single instance of the fastq used in all QA Summary steps.

QACollate extends .QA2. It contains a SimpleList instance with zero or more QASummary elements.

QA extends .QA2, and contains a SimpleList of zero or more QASummary elements. This class represents the results of the qa2 analysis.

Methods

Methods defined on this class include:

qa2

signature(object="QACollate", state, ..., verbose=FALSE) creates a QA report from the elements of QACollate. Methods on qa2 for objects extending class QASummary summarize QA statistics for that class, e.g., qa2,QAFrequentSequences-method implements the calculations required to summarize frequently used sequences, using data in state.

report

signature(x="QA", ...) creates an HTML report. Methods on report for objects extending class QASummary are responsible for creating the html snippet for that QA component.

flag

signature(object=".QA2", ..., verbose=FALSE) implements criteria to flag individual lanes as failing quality assessment. NOTE: flag is not fully implemented.

rbind

signature(...="QASummary"): rbind multiple summary elements of the same class, as when these have been created by separately calculating statistics on a number of fastq files.

show

signature(object = "SolexaExportQA"): Display an overview of the object contents.

Author(s)

Martin Morgan <[e-mail]>

See Also

Specific classes derived from .QA2

Examples

getClass(".QA2", where=getNamespace("ShortRead"))

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