HTSeqCounting: The HTSeqCounting class

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

Description

Package: aroma.seq
Class HTSeqCounting

Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--AromaSeqTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--HTSeqCounting

Directly known subclasses:

public static class HTSeqCounting
extends AromaSeqTransform

...

Usage

HTSeqCounting(dataSet=NULL, transcripts=NULL, ...)

Arguments

dataSet	A BamDataSet.
transcripts	A GtfDataFile specifying a gene model.
...	Arguments passed to AbstractAlignment.

Fields and Methods

Methods:

	getOutputDataSet	-
	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

Supported operating systems

...

Author(s)

Henrik Bengtsson

References

[1] Simon Anders, HTSeq: Analysing high-throughput sequencing data with Python, EMBL, Jan 2014. http://www-huber.embl.de/users/anders/HTSeq/

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