TopHat2Alignment: The TopHat2Alignment class

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

Description

Package: aroma.seq
Class TopHat2Alignment

Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--AromaSeqTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--AbstractAlignment
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--FileGroupsInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--TopHat2Alignment

Directly known subclasses:

public static class TopHat2Alignment
extends FileGroupsInterface

...

Usage

TopHat2Alignment(..., groupBy=NULL, indexSet=NULL, transcripts=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.
transcripts	A GtfDataFile specifying a gene model (transcriptome) GTF/GFF3 file.

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 and macOS [1].

Author(s)

Taku Tokuyasu

References

[1] TopHat - A spliced read mapper for RNA-Seq, 2015. http://ccb.jhu.edu/software/tophat/
[2] Trapnell et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc, 2012.

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