Bowtie2Alignment: The Bowtie2Alignment class

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

Description

Package: aroma.seq
Class Bowtie2Alignment

Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--AromaSeqTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--AbstractAlignment
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--FileGroupsInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--Bowtie2Alignment

Directly known subclasses:

public static class Bowtie2Alignment
extends FileGroupsInterface

...

Usage

Bowtie2Alignment(..., groupBy=NULL, indexSet=NULL)

Arguments

...	Arguments passed to AbstractAlignment.
groupBy	A character string or an explicit named list, specifying which input files should be processed together.
indexSet	An Bowtie2IndexSet.

Fields and Methods

Methods:

	getOutputDataSet	-
	process	-

Methods inherited from FileGroupsInterface:
getGroupBy, getGroupNames, getGroups, getInputDataSet, nbrOfGroups, validateGroups

Methods inherited from AbstractAlignment:
as.character, getAcronym, getAsteriskTags, getIndexSet, getOrganism, getOutputDataSet, getRootPath, isPaired

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

Supported operating systems

This method is available on Linux, macOS, and Windows [1].

Author(s)

Henrik Bengtsson and Pierre Neuvial

References

[1] Bowtie2, John Hopkins University, 2013. http://bowtie-bio.sourceforge.net/bowtie2/

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