QA-class {ShortRead} | R Documentation

## (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 <mtmmorgan@fhcrc.org>

### See Also

Specific classes derived from `.QA2`

### Examples

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

[Package ShortRead version 1.45.4 Index]