AbstractAlignment: The AbstractAlignment class

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

Description

Package: aroma.seq
Class AbstractAlignment

Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--AromaSeqTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--AbstractAlignment

Directly known subclasses:
Bowtie2Alignment, BwaAlignment, TopHat2Alignment

public abstract static class AbstractAlignment
extends AromaSeqTransform

...

Usage

AbstractAlignment(dataSet=NULL, indexSet=NULL, rgSet=NULL, ...)

Arguments

dataSet	An AromaSeqDataFileSet.
indexSet	An AbstractIndexSet.
tags	Additional tags for the output data sets.
rgSet	(optional) An SamReadGroup for added SAM read group to the results.
...	Additional alignment arguments.

Fields and Methods

Methods:
No methods defined.

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

Author(s)

Henrik Bengtsson

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