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

## Documentation for package ‘ShortRead’ version 1.8.2

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.
- Package NEWS.

## Help Pages

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

## -- --

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

## -- --

%in%-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
.ShortReadBase-class | Base classes and methods for high-throughput short-read sequencing
.Solexa-class | Base classes and methods for high-throughput short-read sequencing
.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-method | Quality scores for short reads and their alignments
alphabetByCycle | Summarize short read nucleotide or quality scores by cycle
alphabetByCycle-method | Quality scores for short reads and their alignments
alphabetByCycle-method | "ShortRead" class for short reads
alphabetByCycle-method | "ShortReadQ" class for short reads and their quality scores
alphabetByCycle-method | Summarize short read nucleotide or quality scores by cycle
alphabetFrequency-method | Quality scores for short reads and their alignments
alphabetScore | Efficiently calculate the sum of quality scores across bases
alphabetScore-method | Quality scores for short reads and their alignments
alphabetScore-method | "ShortReadQ" class for short reads and their quality scores
analysisPath | Accessors for ShortRead classes
append-method | "AlignedDataFrame" representing alignment annotations as a data frame
append-method | "AlignedRead" class for aligned short reads
append-method | Quality scores for short reads and their alignments
append-method | "ShortRead" class for short reads
append-method | Base classes and methods for high-throughput short-read sequencing
append-method | "ShortReadQ" class for short reads and their quality scores
ArrayIntensity | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for
ArrayIntensity-class | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for

## -- B --

BAMQA-class | Quality assessment from BAM files
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-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-method | "ShortRead" class for short reads
clean-method | Remove sequences with ambiguous nucleotides from short read classes
coerce-method | "AlignedRead" class for aligned short reads
coerce-method | Quality scores for short reads and their alignments
coerce-method | "ShortReadQ" class for short reads and their quality scores
compact-method | Quality scores for short reads and their alignments
compact-method | "ShortRead" class for short reads
compact-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
coverage-method | "AlignedRead" class for aligned short reads

## -- D --

dataPath | Accessors for ShortRead classes
deprecated | Deprecated and defunct functions
detail-method | "AlignedRead" class for aligned short reads
detail-method | "ExperimentPath" class representing a file hierarchy of data files
detail-method | Quality scores for short reads and their alignments
detail-method | "RochePath" class representing a Roche (454) experiment location
detail-method | A base class for Roche experiment-wide data
detail-method | ".SRUtil" and related classes
detail-method | "ShortRead" class for short reads
detail-method | "ShortReadQ" class for short reads and their quality scores
detail-method | "SolexaPath" class representing a standard output file hierarchy
detail-method | "SolexaSet" coordinating Solexa output locations with sample
dim-method | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for
dim-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-method | Summarize low-complexity sequences

## -- E --

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

## -- 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-class | Quality scores for short reads and their alignments
FastqQuality-method | Construct objects indicating read or alignment quality
FastqSampler | Sampling records from fastq files
FastqSampler-class | Sampling records from fastq files

## -- I --

id | Accessors for ShortRead classes
id-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
Intensity-class | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for
IntensityInfo-class | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for
IntensityMeasure-class | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for

## -- L --

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

## -- 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

## -- N --

name | "SRFilter" for representing functions operating on ShortRead objects
name-method | "SRFilter" for representing functions operating on ShortRead objects
names-method | ".SRUtil" and related classes
names<--method | ".SRUtil" and related classes
narrow-method | Quality scores for short reads and their alignments
narrow-method | "ShortRead" class for short reads
narrow-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

## -- O --

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

## -- P --

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

## -- R --

rbind-method | Virtual class for representing quality assessment results
read454 | "RochePath" class representing a Roche (454) experiment location
read454-method | "RochePath" class representing a Roche (454) experiment location
readAligned | Read aligned reads and their quality scores into R representations
readAligned-method | "SolexaPath" class representing a standard output file hierarchy
readAligned-method | "SolexaSet" coordinating Solexa output locations with sample
readAligned-method | Read aligned reads and their quality scores into R representations
readBaseQuality | Read short reads and their quality scores into R representations
readBaseQuality-method | "RochePath" class representing a Roche (454) experiment location
readBaseQuality-method | "SolexaPath" class representing a standard output file hierarchy
readBaseQuality-method | Read short reads and their quality scores into R representations
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 | Read and write FASTA files to or from ShortRead objects
readFasta-method | "RochePath" class representing a Roche (454) experiment location
readFasta-method | "SolexaPath" class representing a standard output file hierarchy
readFasta-method | Read and write FASTA files to or from ShortRead objects
readFastaQual | "RochePath" class representing a Roche (454) experiment location
readFastaQual-method | "RochePath" class representing a Roche (454) experiment location
readFastq | Read and write FASTQ-formatted files
readFastq-method | "SolexaPath" class representing a standard output file hierarchy
readFastq-method | Read and write FASTQ-formatted files
readIndex | A base class for Roche experiment-wide data
readInfo | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for
readIntensities | Read Illumina image intensity files
readIntensities-method | "SolexaPath" class representing a standard output file hierarchy
readIntensities-method | Read Illumina image intensity files
readPath | "RochePath" class representing a Roche (454) experiment location
readPrb | Read Solexa prb files as fastq-style quality scores
readPrb-method | "SolexaPath" class representing a standard output file hierarchy
readPrb-method | Read Solexa prb files as fastq-style quality scores
readQseq | Read Solexa qseq files as fastq-style quality scores
readQseq-method | "SolexaPath" class representing a standard output file hierarchy
readQseq-method | Read Solexa qseq files as fastq-style quality scores
readQual | "RochePath" class representing a Roche (454) experiment location
readQual-method | "RochePath" class representing a Roche (454) experiment location
readXStringColumns | Read one or more columns into XStringSet (e.g., DNAStringSet) objects
renew | Renew (update) a ShortRead object with new values
renew-method | Renew (update) a ShortRead object with new values
renewable | Renew (update) a ShortRead object with new values
renewable-method | Renew (update) a ShortRead object with new values
report | Summarize quality assessment results into a report
report-method | Quality assessment from BAM files
report-method | Quality assessment summaries from Bowtie files
report-method | Quality assessment of fastq files and ShortReadQ objects
report-method | Quality assessment summaries from MAQ map files
report-method | Quality assessment summaries from Solexa export and realign files
report-method | "SolexaPath" class representing a standard output file hierarchy
report-method | Summarize quality assessment results into a report
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-class | Roche (454) experiment-wide data container
RocheSet-method | "RochePath" class representing a Roche (454) experiment location
RtaIntensity | Construct objects of class "RtaIntensity"
RtaIntensity-class | Class "RtaIntensity"
runNames | "RochePath" class representing a Roche (454) experiment location
runNames-method | "RochePath" class representing a Roche (454) experiment location

## -- S --

Sampler-class | Sampling records from fastq files
sapply-method | ".SRUtil" and related classes
scanPath | Accessors for ShortRead classes
SFastqQuality | Construct objects indicating read or alignment quality
SFastqQuality-class | Quality scores for short reads and their alignments
SFastqQuality-method | Construct objects indicating read or alignment quality
ShortRead | "ShortRead" class for short reads
ShortRead-class | "ShortRead" class for short reads
ShortRead-method | "ShortRead" class for short reads
ShortReadQ | "ShortReadQ" class for short reads and their quality scores
ShortReadQ-class | "ShortReadQ" class for short reads and their quality scores
ShortReadQ-method | "ShortReadQ" class for short reads and their quality scores
ShortReadQQA-class | Quality assessment of fastq files and ShortReadQ objects
show-method | "AlignedRead" class for aligned short reads
show-method | "ExperimentPath" class representing a file hierarchy of data files
show-method | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for
show-method | Virtual class for representing quality assessment results
show-method | Quality scores for short reads and their alignments
show-method | "RochePath" class representing a Roche (454) experiment location
show-method | "SRFilter" for representing functions operating on ShortRead objects
show-method | A base class for Roche experiment-wide data
show-method | ".SRUtil" and related classes
show-method | Sampling records from fastq files
show-method | "ShortRead" class for short reads
show-method | Base classes and methods for high-throughput short-read sequencing
show-method | Quality assessment summaries from Solexa export and realign files
show-method | "SolexaPath" class representing a standard output file hierarchy
show-method | "SolexaSet" coordinating Solexa output locations with sample
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
SolexaSet-class | "SolexaSet" coordinating Solexa output locations with sample
SolexaSet-method | "SolexaPath" class representing a standard output file hierarchy
SolexaSet-method | "SolexaSet" coordinating Solexa output locations with sample
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-method | "ShortRead" class for short reads
srdistance-method | Edit distances between reads and a small number of short references
srdistanceFilter | Functions for user-created and built-in ShortRead filters
srduplicated | Order, sort, and find duplicates in XStringSet objects
srduplicated-method | "AlignedRead" class for aligned short reads
srduplicated-method | Quality scores for short reads and their alignments
srduplicated-method | "ShortRead" class for short reads
srduplicated-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-class | "SRFilter" for representing functions operating on ShortRead objects
srFilter-method | "SRFilter" for representing functions operating on ShortRead objects
srFilter-method | Functions for user-created and built-in ShortRead filters
SRList | ".SRUtil" and related classes
SRList-class | ".SRUtil" and related classes
srorder | Order, sort, and find duplicates in XStringSet objects
srorder-method | "AlignedRead" class for aligned short reads
srorder-method | Quality scores for short reads and their alignments
srorder-method | "ShortRead" class for short reads
srorder-method | Order, sort, and find duplicates in XStringSet objects
srrank | Order, sort, and find duplicates in XStringSet objects
srrank-method | "AlignedRead" class for aligned short reads
srrank-method | Quality scores for short reads and their alignments
srrank-method | "ShortRead" class for short reads
srrank-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-method | Quality scores for short reads and their alignments
srsort-method | "ShortRead" class for short reads
srsort-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-method | "AlignedRead" class for aligned short reads
strandFilter | Functions for user-created and built-in ShortRead filters

## -- T --

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

## -- U --

uniqueFilter | Deprecated functions from the ShortRead package

## -- V --

vclass | Accessors for ShortRead classes

## -- W --

width-method | Quality scores for short reads and their alignments
width-method | "ShortRead" class for short reads
writeFasta | Read and write FASTA files to or from ShortRead objects
writeFasta-method | "ShortRead" class for short reads
writeFastq | Read and write FASTQ-formatted files
writeFastq-method | "ShortReadQ" class for short reads and their quality scores

## -- Y --

yield | Sampling records from fastq files
yield-method | Sampling records from fastq files

## -- misc --

[-method | "AlignedRead" class for aligned short reads
[-method | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for
[-method | Quality scores for short reads and their alignments
[-method | ".SRUtil" and related classes
[-method | "ShortRead" class for short reads
[-method | "ShortReadQ" class for short reads and their quality scores
[-method | Classes "SolexaIntensity" and "SolexaIntensityInfo"
[[-method | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for
[[-method | Quality scores for short reads and their alignments
[[-method | ".SRUtil" and related classes