Base classes and methods for high-throughput short-read sequencing data.

Documentation for package ‘ShortRead’ version 1.0.7

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A B C D E F I L M N P Q R S T V W misc

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ShortReadBase-package

Base classes and methods for high-throughput short-read sequencing data.

-- --

.QA-class	Virtual class for representing quality assessment results
.Roche-class	Base classes and methods for high-throughput short-read sequencing data.
.ShortReadBase-class	Base classes and methods for high-throughput short-read sequencing data.
.Solexa-class	Base classes and methods for high-throughput short-read sequencing data.
.SRUtil-class	".SRUtil" and related classes

-- A --

accessors	Accessors for ShortRead classes
alignData	Accessors for ShortRead classes
alignDataFilter	Functions for user-created and built-in ShortRead filters
AlignedDataFrame	AlignedDataFrame constructor
AlignedDataFrame-class	"AlignedDataFrame" representing alignment annotations as a data frame
AlignedRead	Construct objects of class "AlignedRead"
AlignedRead-class	"AlignedRead" class for aligned short reads
alignQuality	Accessors for ShortRead classes
alignQualityFilter	Functions for user-created and built-in ShortRead filters
alphabet,FastqQuality-method	Quality scores for short reads and their alignments
alphabetByCycle	Summarize short read nucleotide or quality scores by cycle
alphabetByCycle,BStringSet-method	Summarize short read nucleotide or quality scores by cycle
alphabetByCycle,FastqQuality-method	Quality scores for short reads and their alignments
alphabetByCycle,ShortRead-method	"ShortRead" class for short reads
alphabetByCycle,ShortReadQ-method	"ShortReadQ" class for short reads and their quality scores
alphabetFrequency,FastqQuality-method	Quality scores for short reads and their alignments
alphabetScore	Efficiently calculate the sum of quality scoares across bases
alphabetScore,FastqQuality-method	Quality scores for short reads and their alignments
alphabetScore,SFastqQuality-method	Quality scores for short reads and their alignments
alphabetScore,ShortReadQ-method	"ShortReadQ" class for short reads and their quality scores
analysisPath	Accessors for ShortRead classes

-- B --

baseCallPath	Accessors for ShortRead classes
basePath	Deprecated and defunct functions

-- C --

chromosome	Accessors for ShortRead classes
chromosomeFilter	Functions for user-created and built-in ShortRead filters
clean	Remove sequences with ambiguous nucleotides from short read classes
clean,DNAStringSet-method	Remove sequences with ambiguous nucleotides from short read classes
clean,ShortRead-method	"ShortRead" class for short reads
compose	Functions for user-created and built-in ShortRead filters
countLines	Count lines in all (text) files in a directory whose file name matches a pattern
coverage,AlignedRead-method	"AlignedRead" class for aligned short reads

-- D --

dataPath	Accessors for ShortRead classes
deprecated	Deprecated and defunct functions
detail	Show (display) detailed object content
detail,.ShortReadBase-method	".SRUtil" and related classes
detail,AlignedRead-method	"AlignedRead" class for aligned short reads
detail,ExperimentPath-method	"ExperimentPath" class representing a file hierarchy of data files
detail,QualityScore-method	Quality scores for short reads and their alignments
detail,RochePath-method	"RochePath" class representing a Roche (454) experiment location
detail,ShortRead-method	"ShortRead" class for short reads
detail,ShortReadQ-method	"ShortReadQ" class for short reads and their quality scores
detail,SolexaPath-method	"SolexaPath" class representing a standard output file hierarchy
detail,SolexaSet-method	"SolexaSet" coordinating Solexa output locations with sample annotations
detail,SRList-method	".SRUtil" and related classes
detail,SRSet-method	A base class for Roche experiment-wide data
detail,SRVector-method	".SRUtil" and related classes

-- E --

ExperimentPath	"ExperimentPath" class representing a file hierarchy of data files
experimentPath	Accessors for ShortRead classes
experimentPath,SRSet-method	A base class for Roche experiment-wide data
ExperimentPath-class	"ExperimentPath" class representing a file hierarchy of data files

-- F --

FastqQuality	Construct objects indicating read or alignment quality
FastqQuality,BStringSet-method	Construct objects indicating read or alignment quality
FastqQuality,character-method	Construct objects indicating read or alignment quality
FastqQuality,missing-method	Construct objects indicating read or alignment quality
FastqQuality-class	Quality scores for short reads and their alignments

-- I --

id	Accessors for ShortRead classes
imageAnalysisPath	Accessors for ShortRead classes
IntegerQuality	Construct objects indicating read or alignment quality
IntegerQuality-class	Quality scores for short reads and their alignments

-- L --

laneDescription	Accessors for ShortRead classes
laneNames	Accessors for ShortRead classes
laneNames,AnnotatedDataFrame-method	"SolexaSet" coordinating Solexa output locations with sample annotations
laneNames,SolexaSet-method	"SolexaSet" coordinating Solexa output locations with sample annotations
lapply,SRList-method	".SRUtil" and related classes
length,MatrixQuality-method	Quality scores for short reads and their alignments
length,QualityScore-method	Quality scores for short reads and their alignments
length,ShortRead-method	"ShortRead" class for short reads
length,SRList-method	".SRUtil" and related classes

-- M --

MatrixQuality	Construct objects indicating read or alignment quality
MatrixQuality-class	Quality scores for short reads and their alignments

-- N --

name	"SRFilter" for representing functions operating on ShortRead objects
name,SRFilter-method	"SRFilter" for representing functions operating on ShortRead objects
names,SRList-method	".SRUtil" and related classes
names<-,SRList,character-method	".SRUtil" and related classes
nFilter	Functions for user-created and built-in ShortRead filters
NumericQuality	Construct objects indicating read or alignment quality
NumericQuality-class	Quality scores for short reads and their alignments

-- P --

pileup	Calculate a pile-up representation of short-read mappings
polyn	Utilities for common, simple operations
polynFilter	Functions for user-created and built-in ShortRead filters
position	Accessors for ShortRead classes

-- Q --

qa	Perform quality assessment on short reads
qa,character-method	Perform quality assessment on short reads
qa,SolexaPath-method	"SolexaPath" class representing a standard output file hierarchy
QualityScore-class	Quality scores for short reads and their alignments
qualPath	"RochePath" class representing a Roche (454) experiment location

-- R --

read454	"RochePath" class representing a Roche (454) experiment location
read454,RochePath-method	"RochePath" class representing a Roche (454) experiment location
readAligned	Read aligned reads and their quality scores into R representations
readAligned,character-method	Read aligned reads and their quality scores into R representations
readAligned,SolexaPath-method	"SolexaPath" class representing a standard output file hierarchy
readAligned,SolexaSet-method	"SolexaSet" coordinating Solexa output locations with sample annotations
readBaseQuality	Read short reads and their quality scores into R representations
readBaseQuality,character-method	Read short reads and their quality scores into R representations
readBaseQuality,SolexaPath-method	"SolexaPath" class representing a standard output file hierarchy
readBfaToc	Get a list of the sequences in a Maq .bfa file
readCount	A base class for Roche experiment-wide data
readData	A base class for Roche experiment-wide data
readFasta	"RochePath" class representing a Roche (454) experiment location
readFasta,character-method	"RochePath" class representing a Roche (454) experiment location
readFasta,RochePath-method	"RochePath" class representing a Roche (454) experiment location
readFastq	Read FASTQ-formatted files into compact R representations
readFastq,character-method	Read FASTQ-formatted files into compact R representations
readFastq,SolexaPath-method	"SolexaPath" class representing a standard output file hierarchy
readIndex	A base class for Roche experiment-wide data
readPath	"RochePath" class representing a Roche (454) experiment location
readPrb	Read Solexa prb files as fastq-style quality scores
readPrb,character-method	Read Solexa prb files as fastq-style quality scores
readPrb,SolexaPath-method	"SolexaPath" class representing a standard output file hierarchy
readQual	"RochePath" class representing a Roche (454) experiment location
readQual,character-method	"RochePath" class representing a Roche (454) experiment location
readQual,RochePath-method	"RochePath" class representing a Roche (454) experiment location
readXStringColumns	Read one or more columns into XStringSet (e.g., DNAStringSet) objects
report	Summarize quality assessment results into a report
report,character-method	Summarize quality assessment results into a report
report,SolexaExportQA-method	Quality assessment summaries from Solexa export files
report,SolexaPath-method	"SolexaPath" class representing a standard output file hierarchy
RochePath	"RochePath" class representing a Roche (454) experiment location
RochePath-class	"RochePath" class representing a Roche (454) experiment location
RocheSet	Roche (454) experiment-wide data container
RocheSet,character-method	"RochePath" class representing a Roche (454) experiment location
RocheSet,RochePath-method	"RochePath" class representing a Roche (454) experiment location
RocheSet-class	Roche (454) experiment-wide data container
runNames	"RochePath" class representing a Roche (454) experiment location
runNames,RochePath-method	"RochePath" class representing a Roche (454) experiment location

-- S --

sapply,SRList-method	".SRUtil" and related classes
scanPath	Accessors for ShortRead classes
SFastqQuality	Construct objects indicating read or alignment quality
SFastqQuality,BStringSet-method	Construct objects indicating read or alignment quality
SFastqQuality,character-method	Construct objects indicating read or alignment quality
SFastqQuality,missing-method	Construct objects indicating read or alignment quality
SFastqQuality-class	Quality scores for short reads and their alignments
ShortRead-class	"ShortRead" class for short reads
ShortReadQ-class	"ShortReadQ" class for short reads and their quality scores
show,.ShortReadBase-method	Base classes and methods for high-throughput short-read sequencing data.
show,AlignedRead-method	"AlignedRead" class for aligned short reads
show,ExperimentPath-method	"ExperimentPath" class representing a file hierarchy of data files
show,FastqQuality-method	Quality scores for short reads and their alignments
show,NumericQuality-method	Quality scores for short reads and their alignments
show,RochePath-method	"RochePath" class representing a Roche (454) experiment location
show,ShortRead-method	"ShortRead" class for short reads
show,SolexaExportQA-method	Quality assessment summaries from Solexa export files
show,SolexaPath-method	"SolexaPath" class representing a standard output file hierarchy
show,SolexaSet-method	"SolexaSet" coordinating Solexa output locations with sample annotations
show,SRFilter-method	"SRFilter" for representing functions operating on ShortRead objects
show,SRList-method	".SRUtil" and related classes
show,SRSet-method	A base class for Roche experiment-wide data
show,SRVector-method	".SRUtil" and related classes
SolexaExportQA	Quality assessment summaries from Solexa export files
SolexaExportQA-class	Quality assessment summaries from Solexa export files
SolexaPath	"SolexaPath" class representing a standard output file hierarchy
solexaPath	Accessors for ShortRead classes
SolexaPath-class	"SolexaPath" class representing a standard output file hierarchy
SolexaSet	"SolexaSet" coordinating Solexa output locations with sample annotations
SolexaSet,character-method	"SolexaSet" coordinating Solexa output locations with sample annotations
SolexaSet,SolexaPath-method	"SolexaPath" class representing a standard output file hierarchy
SolexaSet-class	"SolexaSet" coordinating Solexa output locations with sample annotations
sourcePath	A base class for Roche experiment-wide data
srapply	Apply-like function for distribution across MPI-based clusters.
srdistance	Edit distances between reads and a small number of short references
srdistance,DNAStringSet,character-method	Edit distances between reads and a small number of short references
srdistance,DNAStringSet,DNAString-method	Edit distances between reads and a small number of short references
srdistance,DNAStringSet,DNAStringSet-method	Edit distances between reads and a small number of short references
srdistance,ShortRead,ANY-method	"ShortRead" class for short reads
srdistanceFilter	Functions for user-created and built-in ShortRead filters
srduplicated	Order, sort, and find duplicates in XStringSet objects
srduplicated,AlignedRead-method	"AlignedRead" class for aligned short reads
srduplicated,FastqQuality-method	Quality scores for short reads and their alignments
srduplicated,ShortRead-method	"ShortRead" class for short reads
srduplicated,XStringSet-method	Order, sort, and find duplicates in XStringSet objects
sread	Accessors for ShortRead classes
SRError	".SRUtil" and related classes
SRError-class	".SRUtil" and related classes
srFilter	Functions for user-created and built-in ShortRead filters
srFilter,function-method	Functions for user-created and built-in ShortRead filters
srFilter,missing-method	Functions for user-created and built-in ShortRead filters
srFilter,SRFilter-method	"SRFilter" for representing functions operating on ShortRead objects
SRFilter-class	"SRFilter" for representing functions operating on ShortRead objects
SRList	".SRUtil" and related classes
SRList-class	".SRUtil" and related classes
srorder	Order, sort, and find duplicates in XStringSet objects
srorder,AlignedRead-method	"AlignedRead" class for aligned short reads
srorder,FastqQuality-method	Quality scores for short reads and their alignments
srorder,ShortRead-method	"ShortRead" class for short reads
srorder,XStringSet-method	Order, sort, and find duplicates in XStringSet objects
srrank	Order, sort, and find duplicates in XStringSet objects
srrank,AlignedRead-method	"AlignedRead" class for aligned short reads
srrank,FastqQuality-method	Quality scores for short reads and their alignments
srrank,ShortRead-method	"ShortRead" class for short reads
srrank,XStringSet-method	Order, sort, and find duplicates in XStringSet objects
SRSet-class	A base class for Roche experiment-wide data
srsort	Order, sort, and find duplicates in XStringSet objects
srsort,FastqQuality-method	Quality scores for short reads and their alignments
srsort,ShortRead-method	"ShortRead" class for short reads
srsort,XStringSet-method	Order, sort, and find duplicates in XStringSet objects
SRVector	".SRUtil" and related classes
SRVector-class	".SRUtil" and related classes
SRWarn	".SRUtil" and related classes
SRWarn-class	".SRUtil" and related classes
strand,AlignedRead-method	"AlignedRead" class for aligned short reads
strandFilter	Functions for user-created and built-in ShortRead filters

-- T --

tables	Summarize XStringSet read frequencies
tables,ShortRead-method	"ShortRead" class for short reads
tables,XStringSet-method	Summarize XStringSet read frequencies

-- V --

vclass

Accessors for ShortRead classes

-- W --

width,FastqQuality-method	Quality scores for short reads and their alignments
width,MatrixQuality-method	Quality scores for short reads and their alignments
width,NumericQuality-method	Quality scores for short reads and their alignments
width,QualityScore-method	Quality scores for short reads and their alignments
width,ShortRead-method	"ShortRead" class for short reads

-- misc --

[,AlignedRead,ANY,ANY,ANY-method	"AlignedRead" class for aligned short reads
[,AlignedRead,ANY,missing,ANY-method	"AlignedRead" class for aligned short reads
[,AlignedRead,missing,ANY,ANY-method	"AlignedRead" class for aligned short reads
[,AlignedRead,missing,missing,ANY-method	"AlignedRead" class for aligned short reads
[,MatrixQuality,ANY,missing,ANY-method	Quality scores for short reads and their alignments
[,QualityScore,ANY,missing,ANY-method	Quality scores for short reads and their alignments
[,ShortRead,ANY,ANY,ANY-method	"ShortRead" class for short reads
[,ShortRead,ANY,missing,ANY-method	"ShortRead" class for short reads
[,ShortRead,missing,ANY,ANY-method	"ShortRead" class for short reads
[,ShortRead,missing,missing,ANY-method	"ShortRead" class for short reads
[,ShortReadQ,ANY,ANY,ANY-method	"ShortReadQ" class for short reads and their quality scores
[,ShortReadQ,ANY,missing,ANY-method	"ShortReadQ" class for short reads and their quality scores
[,ShortReadQ,missing,ANY,ANY-method	"ShortReadQ" class for short reads and their quality scores
[,ShortReadQ,missing,missing,ANY-method	"ShortReadQ" class for short reads and their quality scores
[,SRList,ANY,missing,ANY-method	".SRUtil" and related classes
[[,MatrixQuality,ANY,missing-method	Quality scores for short reads and their alignments
[[,QualityScore,ANY,missing-method	Quality scores for short reads and their alignments
[[,SRList,ANY,missing-method	".SRUtil" and related classes