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


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Documentation for package ‘ShortRead’ version 1.2.1

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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 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
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,FastqQuality,matrix-method Quality scores for short reads and their alignments
coerce,FastqQuality,numeric-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
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 summaries from MAQ map files
FastqQA-class Quality assessment summaries from MAQ map files
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
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 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
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,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 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 summaries from MAQ map files
report,MAQMapQA-method Quality assessment summaries from MAQ map files
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
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
show,.QA-method Quality assessment summaries from Solexa export files
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 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
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
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