QDNAseqEstimation: The QDNAseqEstimation class

In HenrikBengtsson/aroma.seq: High-Throughput Sequence Analysis using the Aroma Framework

Description

Package: aroma.seq
Class QDNAseqEstimation

Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--AromaSeqTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--QDNAseqEstimation

Directly known subclasses:

public static class QDNAseqEstimation
extends AromaSeqTransform

Usage

QDNAseqEstimation(dataSet=NULL, binWidth=NULL, log=TRUE, mappability=50, blacklist=0,
  residual=2, bases=0, ...)

Arguments

dataSet	An BamDataSet.
binWidth	A positive numeric specifying the bin width (in units of kbp). Alternatively, a AnnotatedDataFrame specifying the bins.
log	If TRUE, the copy numbers are calculated on the log2 scale.
mappability, blacklist, residual, bases	Post-filter arguments.
...	Additional arguments passed to the QDNAseq method.

Fields and Methods

Methods:

	process	-

Methods inherited from AromaSeqTransform:
as.character, findFilesTodo, getAcronym, getAsteriskTags, getFlavor, getFullName, getInputDataSet, getName, getOptionalArguments, getOrganism, getOutputDataSet, getParameters, getPath, getRootPath, getTags, isDone, length, process, setTags

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, findRspReportTemplate, asThis

Benchmarking

TBA.

Author(s)

Henrik Bengtsson

References

[1] TBA.

HenrikBengtsson/aroma.seq documentation built on Feb. 15, 2021, 2:21 a.m.