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

## Documentation for package ‘ShortRead’ version 1.4.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

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

## -- --

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

## -- --

%in%,AlignedRead,RangesList-method | "AlignedRead" class for aligned short reads
.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 scores 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
append,.ShortReadBase,.ShortReadBase,ANY-method | Base classes and methods for high-throughput short-read sequencing data.
append,AlignedDataFrame,AlignedDataFrame,missing-method | "AlignedDataFrame" representing alignment annotations as a data frame
append,AlignedRead,AlignedRead,missing-method | "AlignedRead" class for aligned short reads
append,MatrixQuality,MatrixQuality,missing-method | Quality scores for short reads and their alignments
append,QualityScore,QualityScore,missing-method | Quality scores for short reads and their alignments
append,ShortRead,ShortRead,missing-method | "ShortRead" class for short reads
append,ShortReadQ,ShortReadQ,missing-method | "ShortReadQ" class for short reads and their quality scores
ArrayIntensity | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities
ArrayIntensity-class | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities

## -- B --

baseCallPath | Accessors for ShortRead classes
basePath | Deprecated and defunct functions
BowtieQA-class | Quality assessment summaries from Bowtie files

## -- C --

chromosome | Accessors for ShortRead classes
chromosome,AlignedRead-method | "AlignedRead" class for aligned short reads
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
coerce,AlignedRead,RangesList-method | "AlignedRead" class for aligned short reads
coerce,FastqQuality,matrix-method | Quality scores for short reads and their alignments
coerce,FastqQuality,numeric-method | Quality scores for short reads and their alignments
coerce,FastqQuality,PhredQuality-method | Quality scores for short reads and their alignments
coerce,PairwiseAlignedXStringSet,AlignedRead-method | "AlignedRead" class for aligned short reads
coerce,SFastqQuality,matrix-method | Quality scores for short reads and their alignments
coerce,SFastqQuality,SolexaQuality-method | Quality scores for short reads and their alignments
coerce,ShortReadQ,QualityScaledDNAStringSet-method | "ShortReadQ" class for short reads and their quality scores
compact,FastqQuality-method | Quality scores for short reads and their alignments
compact,ShortRead-method | "ShortRead" class for short reads
compact,ShortReadQ-method | "ShortReadQ" class for short reads and their quality scores
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
dim,Intensity-method | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities
dim,MatrixQuality-method | Quality scores for short reads and their alignments
dustyFilter | Functions for user-created and built-in ShortRead filters
dustyScore | Summarize low-complexity sequences
dustyScore,DNAStringSet-method | Summarize low-complexity sequences
dustyScore,ShortRead-method | Summarize low-complexity sequences

## -- 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 --

FastqQA | Quality assessment of fastq files and ShortReadQ objects
FastqQA-class | Quality assessment of fastq files and ShortReadQ objects
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
id,ShortRead-method | "ShortRead" class for short reads
idFilter | Functions for user-created and built-in ShortRead filters
imageAnalysisPath | Accessors for ShortRead classes
IntegerQuality | Construct objects indicating read or alignment quality
IntegerQuality-class | Quality scores for short reads and their alignments
intensity | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities
Intensity-class | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities
IntensityInfo-class | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities
IntensityMeasure-class | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities

## -- 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,ANY-method | ".SRUtil" and related classes
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 --

MAQMapQA | Quality assessment summaries from MAQ map files
MAQMapQA-class | Quality assessment summaries from MAQ map files
MatrixQuality | Construct objects indicating read or alignment quality
MatrixQuality-class | Quality scores for short reads and their alignments
measurementError | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities

## -- 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
narrow,FastqQuality-method | Quality scores for short reads and their alignments
narrow,MatrixQuality-method | Quality scores for short reads and their alignments
narrow,ShortRead-method | "ShortRead" class for short reads
narrow,ShortReadQ-method | "ShortReadQ" class for short reads and their quality scores
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 --

phenoData,SRSet-method | A base class for Roche experiment-wide data
pileup | Deprecated and defunct functions
polyn | Utilities for common, simple operations
polynFilter | Functions for user-created and built-in ShortRead filters
position | Accessors for ShortRead classes
position,AlignedRead-method | "AlignedRead" class for aligned short reads
positionFilter | Functions for user-created and built-in ShortRead filters

## -- Q --

qa | Perform quality assessment on short reads
qa,character-method | Perform quality assessment on short reads
qa,list-method | Perform quality assessment on short reads
qa,ShortReadQ-method | "ShortReadQ" class for short reads and their quality scores
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 --

rbind,.QA-method | Virtual class for representing quality assessment results
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,RochePath-method | "RochePath" class representing a Roche (454) experiment location
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
readFastaQual | "RochePath" class representing a Roche (454) experiment location
readFastaQual,character-method | "RochePath" class representing a Roche (454) experiment location
readFastaQual,RochePath-method | "RochePath" class representing a Roche (454) experiment location
readFastq | Read and write FASTQ-formatted files
readFastq,character-method | Read and write FASTQ-formatted files
readFastq,SolexaPath-method | "SolexaPath" class representing a standard output file hierarchy
readIndex | A base class for Roche experiment-wide data
readInfo | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities
readIntensities | Read Solexa 'int' and 'nse' files
readIntensities,character-method | Read Solexa 'int' and 'nse' files
readIntensities,SolexaPath-method | "SolexaPath" class representing a standard output file hierarchy
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
readQseq | Read Solexa qseq files as fastq-style quality scores
readQseq,character-method | Read Solexa qseq files as fastq-style quality scores
readQseq,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,ANY-method | Summarize quality assessment results into a report
report,BowtieQA-method | Quality assessment summaries from Bowtie files
report,FastqQA-method | Quality assessment of fastq files and ShortReadQ objects
report,MAQMapQA-method | Quality assessment summaries from MAQ map files
report,SolexaExportQA-method | Quality assessment summaries from Solexa export and realign 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 | "ShortRead" class for short reads
ShortRead,DNAStringSet,BStringSet-method | "ShortRead" class for short reads
ShortRead,DNAStringSet,missing-method | "ShortRead" class for short reads
ShortRead,missing,missing-method | "ShortRead" class for short reads
ShortRead-class | "ShortRead" class for short reads
ShortReadQ | "ShortReadQ" class for short reads and their quality scores
ShortReadQ,DNAStringSet,QualityScore,BStringSet-method | "ShortReadQ" class for short reads and their quality scores
ShortReadQ,DNAStringSet,QualityScore,missing-method | "ShortReadQ" class for short reads and their quality scores
ShortReadQ,missing,missing,missing-method | "ShortReadQ" class for short reads and their quality scores
ShortReadQ-class | "ShortReadQ" class for short reads and their quality scores
ShortReadQQA-class | Quality assessment of fastq files and ShortReadQ objects
show,.QA-method | Virtual class for representing quality assessment results
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,Intensity-method | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities
show,IntensityMeasure-method | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities
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 and realign 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 and realign files
SolexaExportQA-class | Quality assessment summaries from Solexa export and realign files
SolexaIntensity | Construct objects of class "SolexaIntensity" and "SolexaIntensityInfo"
SolexaIntensity-class | Classes "SolexaIntensity" and "SolexaIntensityInfo"
SolexaIntensityInfo | Construct objects of class "SolexaIntensity" and "SolexaIntensityInfo"
SolexaIntensityInfo-class | Classes "SolexaIntensity" and "SolexaIntensityInfo"
SolexaPath | "SolexaPath" class representing a standard output file hierarchy
solexaPath | Accessors for ShortRead classes
SolexaPath-class | "SolexaPath" class representing a standard output file hierarchy
SolexaRealignQA-class | Quality assessment summaries from Solexa export and realign files
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
trimLRPatterns,ShortRead-method | "ShortRead" class for short reads

## -- U --

uniqueFilter | Functions for user-created and built-in ShortRead filters

## -- 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
writeFastq | Read and write FASTQ-formatted files
writeFastq,ShortReadQ-method | "ShortReadQ" class for short reads and their quality scores

## -- misc --

[,AlignedRead,ANY,ANY,ANY-method | "AlignedRead" class for aligned short reads
[,AlignedRead,ANY,ANY-method | "AlignedRead" class for aligned short reads
[,AlignedRead,ANY,missing,ANY-method | "AlignedRead" class for aligned short reads
[,AlignedRead,ANY,missing-method | "AlignedRead" class for aligned short reads
[,AlignedRead,missing,ANY,ANY-method | "AlignedRead" class for aligned short reads
[,AlignedRead,missing,ANY-method | "AlignedRead" class for aligned short reads
[,AlignedRead,missing,missing,ANY-method | "AlignedRead" class for aligned short reads
[,AlignedRead,missing,missing-method | "AlignedRead" class for aligned short reads
[,IntensityMeasure,ANY,ANY,ANY-method | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities
[,IntensityMeasure,ANY,ANY-method | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities
[,IntensityMeasure,ANY,missing,ANY-method | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities
[,IntensityMeasure,missing,ANY,ANY-method | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities
[,IntensityMeasure,missing,missing,ANY-method | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities
[,MatrixQuality,ANY,missing,ANY-method | Quality scores for short reads and their alignments
[,MatrixQuality,ANY,missing-method | Quality scores for short reads and their alignments
[,QualityScore,ANY,missing,ANY-method | Quality scores for short reads and their alignments
[,QualityScore,ANY,missing-method | Quality scores for short reads and their alignments
[,ShortRead,ANY,ANY,ANY-method | "ShortRead" class for short reads
[,ShortRead,ANY,ANY-method | "ShortRead" class for short reads
[,ShortRead,ANY,missing,ANY-method | "ShortRead" class for short reads
[,ShortRead,ANY,missing-method | "ShortRead" class for short reads
[,ShortRead,missing,ANY,ANY-method | "ShortRead" class for short reads
[,ShortRead,missing,ANY-method | "ShortRead" class for short reads
[,ShortRead,missing,missing,ANY-method | "ShortRead" class for short reads
[,ShortRead,missing,missing-method | "ShortRead" class for short reads
[,ShortReadQ,ANY,ANY,ANY-method | "ShortReadQ" class for short reads and their quality scores
[,ShortReadQ,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,ANY,missing-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,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
[,ShortReadQ,missing,missing-method | "ShortReadQ" class for short reads and their quality scores
[,SolexaIntensity,ANY,ANY,ANY-method | Classes "SolexaIntensity" and "SolexaIntensityInfo"
[,SolexaIntensity,ANY,ANY-method | Classes "SolexaIntensity" and "SolexaIntensityInfo"
[,SolexaIntensity,ANY,missing,ANY-method | Classes "SolexaIntensity" and "SolexaIntensityInfo"
[,SolexaIntensity,missing,ANY,ANY-method | Classes "SolexaIntensity" and "SolexaIntensityInfo"
[,SolexaIntensity,missing,missing,ANY-method | Classes "SolexaIntensity" and "SolexaIntensityInfo"
[,SRList,ANY,missing,ANY-method | ".SRUtil" and related classes
[,SRList,ANY,missing-method | ".SRUtil" and related classes
[[,ArrayIntensity,ANY,ANY-method | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities
[[,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