Entry: AlignedDataFrame-class
Aliases: AlignedDataFrame-class
Keywords: classes
Description: "AlignedDataFrame" representing alignment annotations as a data frame
URL: ../../../library/ShortRead/html/AlignedDataFrame-class.html

Entry: AlignedDataFrame
Aliases: AlignedDataFrame
Keywords: manip
Description: AlignedDataFrame constructor
URL: ../../../library/ShortRead/html/AlignedDataFrame.html

Entry: AlignedRead-class
Aliases: AlignedRead-class [,AlignedRead,missing,missing,ANY-method [,AlignedRead,missing,ANY,ANY-method [,AlignedRead,ANY,ANY,ANY-method [,AlignedRead,ANY,missing,ANY-method strand,AlignedRead-method coverage,AlignedRead-method srrank,AlignedRead-method srorder,AlignedRead-method srduplicated,AlignedRead-method detail,AlignedRead-method show,AlignedRead-method
Keywords: classes
Description: "AlignedRead" class for aligned short reads
URL: ../../../library/ShortRead/html/AlignedRead-class.html

Entry: AlignedRead
Aliases: AlignedRead
Keywords: manip
Description: Construct objects of class "AlignedRead"
URL: ../../../library/ShortRead/html/AlignedRead.html

Entry: ExperimentPath-class
Aliases: ExperimentPath-class ExperimentPath show,ExperimentPath-method detail,ExperimentPath-method
Keywords: classes
Description: "ExperimentPath" class representing a file hierarchy of data files
URL: ../../../library/ShortRead/html/ExperimentPath-class.html

Entry: .QA-class
Aliases: .QA-class
Keywords: classes
Description: Virtual class for representing quality assessment results
URL: ../../../library/ShortRead/html/QA-class.html

Entry: QualityScore-class
Aliases: QualityScore-class NumericQuality-class IntegerQuality-class MatrixQuality-class FastqQuality-class SFastqQuality-class [,QualityScore,ANY,missing,ANY-method [[,QualityScore,ANY,missing-method length,QualityScore-method width,QualityScore-method detail,QualityScore-method width,NumericQuality-method show,NumericQuality-method [,MatrixQuality,ANY,missing,ANY-method [[,MatrixQuality,ANY,missing-method length,MatrixQuality-method width,MatrixQuality-method width,FastqQuality-method show,FastqQuality-method alphabet,FastqQuality-method alphabetFrequency,FastqQuality-method alphabetByCycle,FastqQuality-method alphabetScore,FastqQuality-method srsort,FastqQuality-method srorder,FastqQuality-method srrank,FastqQuality-method srduplicated,FastqQuality-method alphabetScore,SFastqQuality-method
Keywords: classes
Description: Quality scores for short reads and their alignments
URL: ../../../library/ShortRead/html/QualityScore-class.html

Entry: QualityScore
Aliases: NumericQuality IntegerQuality MatrixQuality FastqQuality FastqQuality,BStringSet-method FastqQuality,character-method FastqQuality,missing-method SFastqQuality SFastqQuality,BStringSet-method SFastqQuality,character-method SFastqQuality,missing-method
Keywords: manip
Description: Construct objects indicating read or alignment quality
URL: ../../../library/ShortRead/html/QualityScore.html

Entry: RochePath-class
Aliases: RochePath-class detail,RochePath-method read454,RochePath-method readFasta readFasta,character-method readFasta,RochePath-method readPath readQual readQual,character-method readQual,RochePath-method read454 runNames qualPath runNames,RochePath-method RocheSet,character-method RocheSet,RochePath-method runNames,RochePath-method show,RochePath-method RochePath
Keywords: classes
Description: "RochePath" class representing a Roche (454) experiment location
URL: ../../../library/ShortRead/html/RochePath-class.html

Entry: RocheSet-class
Aliases: RocheSet-class RocheSet
Keywords: classes
Description: Roche (454) experiment-wide data container
URL: ../../../library/ShortRead/html/RocheSet-class.html

Entry: SRFilter-class
Aliases: SRFilter-class srFilter,SRFilter-method name name,SRFilter-method show,SRFilter-method
Keywords: classes
Description: "SRFilter" for representing functions operating on ShortRead objects
URL: ../../../library/ShortRead/html/SRFilter-class.html

Entry: SRSet-class
Aliases: SRSet-class readCount readData readIndex sourcePath experimentPath,SRSet-method show,SRSet-method detail,SRSet-method
Keywords: classes
Description: A base class for Roche experiment-wide data
URL: ../../../library/ShortRead/html/SRSet-class.html

Entry: SRUtil-class
Aliases: .SRUtil-class SRError-class SRWarn-class SRList-class SRVector-class SRError SRWarn SRList SRVector detail,.ShortReadBase-method length,SRList-method names,SRList-method names<-,SRList,character-method lapply,SRList-method sapply,SRList-method [,SRList,ANY,missing,ANY-method [[,SRList,ANY,missing-method detail,SRList-method show,SRList-method detail,SRVector-method show,SRVector-method
Keywords: classes
Description: ".SRUtil" and related classes
URL: ../../../library/ShortRead/html/SRUtil-class.html

Entry: ShortRead-class
Aliases: ShortRead-class srrank,ShortRead-method srorder,ShortRead-method srsort,ShortRead-method srduplicated,ShortRead-method srdistance,ShortRead,ANY-method alphabetByCycle,ShortRead-method tables,ShortRead-method clean,ShortRead-method [,ShortRead,missing,missing,ANY-method [,ShortRead,missing,ANY,ANY-method [,ShortRead,ANY,ANY,ANY-method [,ShortRead,ANY,missing,ANY-method detail,ShortRead-method length,ShortRead-method show,ShortRead-method width,ShortRead-method
Keywords: classes
Description: "ShortRead" class for short reads
URL: ../../../library/ShortRead/html/ShortRead-class.html

Entry: ShortReadBase-package
Aliases: ShortReadBase-package .ShortReadBase-class show,.ShortReadBase-method .Solexa-class .Roche-class
Keywords: package
Description: Base classes and methods for high-throughput short-read sequencing data.
URL: ../../../library/ShortRead/html/ShortRead-package.html

Entry: ShortReadQ-class
Aliases: ShortReadQ-class alphabetByCycle,ShortReadQ-method alphabetScore,ShortReadQ-method [,ShortReadQ,missing,missing,ANY-method [,ShortReadQ,missing,ANY,ANY-method [,ShortReadQ,ANY,ANY,ANY-method [,ShortReadQ,ANY,missing,ANY-method detail,ShortReadQ-method
Keywords: classes
Description: "ShortReadQ" class for short reads and their quality scores
URL: ../../../library/ShortRead/html/ShortReadQ-class.html

Entry: SolexaExportQA-class
Aliases: SolexaExportQA SolexaExportQA-class report,SolexaExportQA-method show,SolexaExportQA-method
Keywords: classes
Description: Quality assessment summaries from Solexa export files
URL: ../../../library/ShortRead/html/SolexaExportQA-class.html

Entry: SolexaPath-class
Aliases: SolexaPath-class SolexaPath SolexaSet,SolexaPath-method qa,SolexaPath-method report,SolexaPath-method show,SolexaPath-method detail,SolexaPath-method readPrb,SolexaPath-method readFastq,SolexaPath-method readBaseQuality,SolexaPath-method readAligned,SolexaPath-method
Keywords: classes
Description: "SolexaPath" class representing a standard output file hierarchy
URL: ../../../library/ShortRead/html/SolexaPath-class.html

Entry: SolexaSet-class
Aliases: SolexaSet-class SolexaSet SolexaSet,character-method detail,SolexaSet-method laneNames,SolexaSet-method laneNames,AnnotatedDataFrame-method show,SolexaSet-method readAligned,SolexaSet-method
Keywords: classes
Description: "SolexaSet" coordinating Solexa output locations with sample annotations
URL: ../../../library/ShortRead/html/SolexaSet-class.html

Entry: accessors
Aliases: accessors vclass sread id chromosome position alignQuality alignData experimentPath dataPath scanPath imageAnalysisPath baseCallPath analysisPath solexaPath laneDescription laneNames
Keywords: manip
Description: Accessors for ShortRead classes
URL: ../../../library/ShortRead/html/accessors.html

Entry: alphabetByCycle
Aliases: alphabetByCycle alphabetByCycle,BStringSet-method
Keywords: manip
Description: Summarize short read nucleotide or quality scores by cycle
URL: ../../../library/ShortRead/html/alphabetByCycle.html

Entry: alphabetScore
Aliases: alphabetScore
Keywords: manip
Description: Efficiently calculate the sum of quality scoares across bases
URL: ../../../library/ShortRead/html/alphabetScore.html

Entry: clean
Aliases: clean clean,DNAStringSet-method
Keywords: manip
Description: Remove sequences with ambiguous nucleotides from short read classes
URL: ../../../library/ShortRead/html/clean.html

Entry: countLines
Aliases: countLines
Keywords: manip
Description: Count lines in all (text) files in a directory whose file name matches a pattern
URL: ../../../library/ShortRead/html/countLines.html

Entry: deprecated
Aliases: deprecated basePath
Keywords: manip
Description: Deprecated and defunct functions
URL: ../../../library/ShortRead/html/deprecated.html

Entry: detail
Aliases: detail
Keywords: manip
Description: Show (display) detailed object content
URL: ../../../library/ShortRead/html/detail.html

Entry: pileup
Aliases: pileup
Keywords: 
Description: Calculate a pile-up representation of short-read mappings
URL: ../../../library/ShortRead/html/pileup.html

Entry: Utilites
Aliases: polyn
Keywords: manip
Description: Utilities for common, simple operations
URL: ../../../library/ShortRead/html/polyn.html

Entry: qa
Aliases: qa qa,character-method
Keywords: manip
Description: Perform quality assessment on short reads
URL: ../../../library/ShortRead/html/qa.html

Entry: readAligned
Aliases: readAligned readAligned,character-method
Keywords: manip
Description: Read aligned reads and their quality scores into R representations
URL: ../../../library/ShortRead/html/readAligned.html

Entry: readBaseQuality
Aliases: readBaseQuality readBaseQuality,character-method
Keywords: manip
Description: Read short reads and their quality scores into R representations
URL: ../../../library/ShortRead/html/readBaseQuality.html

Entry: readBfaToc
Aliases: readBfaToc
Keywords: 
Description: Get a list of the sequences in a Maq .bfa file
URL: ../../../library/ShortRead/html/readBfaToc.html

Entry: readFastq
Aliases: readFastq readFastq,character-method
Keywords: manip
Description: Read FASTQ-formatted files into compact R representations
URL: ../../../library/ShortRead/html/readFastq.html

Entry: readPrb
Aliases: readPrb readPrb,character-method
Keywords: manip
Description: Read Solexa prb files as fastq-style quality scores
URL: ../../../library/ShortRead/html/readPrb.html

Entry: readXStringColumns
Aliases: readXStringColumns
Keywords: IO
Description: Read one or more columns into XStringSet (e.g., DNAStringSet) objects
URL: ../../../library/ShortRead/html/readXStringColumns.html

Entry: report
Aliases: report report,character-method
Keywords: manip
Description: Summarize quality assessment results into a report
URL: ../../../library/ShortRead/html/report.html

Entry: srFilter
Aliases: srFilter srFilter,missing-method srFilter,function-method chromosomeFilter strandFilter nFilter polynFilter srdistanceFilter alignQualityFilter alignDataFilter compose
Keywords: manip
Description: Functions for user-created and built-in ShortRead filters
URL: ../../../library/ShortRead/html/srFilter.html

Entry: srapply
Aliases: srapply
Keywords: manip
Description: Apply-like function for distribution across MPI-based clusters.
URL: ../../../library/ShortRead/html/srapply.html

Entry: srdistance
Aliases: srdistance srdistance,DNAStringSet,character-method srdistance,DNAStringSet,DNAString-method srdistance,DNAStringSet,DNAStringSet-method
Keywords: manip
Description: Edit distances between reads and a small number of short references
URL: ../../../library/ShortRead/html/srdistance.html

Entry: srduplicated
Aliases: srorder srrank srsort srduplicated srorder,XStringSet-method srrank,XStringSet-method srsort,XStringSet-method srduplicated,XStringSet-method
Keywords: manip
Description: Order, sort, and find duplicates in XStringSet objects
URL: ../../../library/ShortRead/html/srduplicated.html

Entry: tables
Aliases: tables tables,XStringSet-method
Keywords: manip
Description: Summarize XStringSet read frequencies
URL: ../../../library/ShortRead/html/tables.html
