BamDataSet: The BamDataSet class

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

Description

Package: aroma.seq
Class BamDataSet

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFileSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--AromaPathnameInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--AromaSeqDataFileSet
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--BamDataSet

Directly known subclasses:

public static class BamDataSet
extends AromaSeqDataFileSet

An BamDataSet object represents a set of BamDataFile:s.

Usage

BamDataSet(files=NULL, ...)

Arguments

files	A list of BamDataFile:s.
...	Arguments passed to GenericDataFileSet.

Fields and Methods

Methods:

	as.character	-
	byName	-
	byPath	-
	convertToSam	-
	countNucleotides	-
	doDownsample	-
	doHTSeqCount	-
	doQDNAseq	-
	findByName	-
	getChipType	-
	getPlatform	-
	isPaired	-
	mpileup	-
	sortByName	-
	sortByPosition	-
	splitByTargetType	-

Methods inherited from AromaSeqDataFileSet:
doBWA, getDefaultFullName, isCompatibleWith

Methods inherited from AromaPathnameInterface:
directoryStructure, getOrganism

Methods inherited from GenericDataFileSet:
[, [[, anyDuplicated, anyNA, append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByNULL, appendFullNamesTranslatorByTabularTextFile, appendFullNamesTranslatorByTabularTextFileSet, appendFullNamesTranslatorBydata.frame, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, as.character, as.list, byName, byPath, c, clearCache, clearFullNamesTranslator, clone, copyTo, dsApplyInPairs, duplicated, equals, extract, findByName, findDuplicated, getChecksum, getChecksumFileSet, getChecksumObjects, getDefaultFullName, getFile, getFileClass, getFileSize, getFiles, getFullNames, getNames, getOneFile, getPath, getPathnames, getSubdirs, gunzip, gzip, hasFile, indexOf, is.na, names, nbrOfFiles, rep, resetFullNames, setFullNamesTranslator, sortBy, unique, update2, updateFullName, updateFullNames, validate, directoryItem, directoryItems, directoryStructure, directoryStructure<-, updateDirectoryStructure, getFullNameTranslatorSet, getParentName

Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName

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.