FastqDataSet: The FastqDataSet class

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

Description

Package: aroma.seq
Class FastqDataSet

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

Directly known subclasses:
IlluminaFastqDataSet, PairedEndFastqDataSet

public static class FastqDataSet
extends AromaSeqDataFileSet

An FastqDataSet object represents a set of FastqDataFile:s.

Usage

FastqDataSet(files=NULL, ..., paired=FALSE, struct=NULL)

Arguments

files	A list of FastqDataFile:s.
...	Arguments passed to GenericDataFileSet.
paired	If TRUE, the data set contains paired-end reads, otherwise not.
struct	A directory structure format.

Fields and Methods

Methods:

	byName	-
	doBowtie2	-
	doDownsample	-
	doQDNAseq	-
	doTopHat2	-
	findByName	-
	getDefaultSamReadGroup	-
	getSamReadGroup	-
	report	-
	setSamReadGroup	-

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

Paired reads

There is a community/industry convention for paired-end runs: "The reads are reported two FASTQ files, such that the n:th read in the first file is mate-paired to the n:th read in the second file. The read IDs must match." [1]

If argument paired=TRUE, the files arguments is assumed to contain the "R1" files whereas the corresponding "R2" files are implicit (inferred and located by matching the filenames).

Author(s)

Henrik Bengtsson

References

[1] Simon Anders, High-throughput sequencing: Alignment and related topic, (38 slides), EMBL Heidelberg, June 2013.

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