Classes derived from .QA-class represent results of quality
assurance analyses.
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. .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. 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.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.signature(object=".QA2", ..., verbose=FALSE)
implements criteria to flag individual lanes as failing quality
assessment. NOTE: flag is not fully implemented.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.signature(object = "SolexaExportQA"): Display an
overview of the object contents..QA2
getClass(".QA2", where=getNamespace("ShortRead"))
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