FASTQ input and manipulation

---

Documentation for package ‘ShortRead’ version 1.56.1

• DESCRIPTION file.
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A B C D E F G I L M N O P Q R S T U V W Y Z misc

ShortReadBase-package

FASTQ input and manipulation.

-- A --

accessors	(Legacy) Accessors for ShortRead classes
alignData	(Legacy) Accessors for ShortRead classes
alignDataFilter	Functions for user-created and built-in ShortRead filters
AlignedDataFrame	(Legacy) AlignedDataFrame constructor
AlignedDataFrame-class	(Legacy) "AlignedDataFrame" representing alignment annotations as a data frame
AlignedRead	(Legacy) Construct objects of class "AlignedRead"
AlignedRead-class	(Legacy) "AlignedRead" class for aligned short reads
alignQuality	(Legacy) 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 nucleotide, amino acid, 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 nucleotide, amino acid, 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	(Legacy) Accessors for ShortRead classes
annTrack	Class '"Snapshot"'
annTrack-method	Class '"Snapshot"'
append-method	(Legacy) "AlignedDataFrame" representing alignment annotations as a data frame
append-method	(Legacy) "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	FASTQ input and manipulation.
append-method	"ShortReadQ" class for short reads and their quality scores
ArrayIntensity	(Legacy) "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities
ArrayIntensity-class	(Legacy) "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities

-- B --

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

-- C --

c-method	"SRFilter" for representing functions operating on ShortRead objects
chromosome	(Legacy) Accessors for ShortRead classes
chromosome-method	(Legacy) "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
close.ShortReadFile	Sampling and streaming records from fastq files
coerce-method	(Legacy) "AlignedRead" class for aligned short reads
coerce-method	Quality scores for short reads and their alignments
coerce-method	"SRFilter" for representing functions operating on ShortRead objects
coerce-method	"ShortRead" class for short reads
coerce-method	"ShortReadQ" class for short reads and their quality scores
compose	Functions for user-created and built-in ShortRead filters
countFastq	Read, write, and count records in FASTQ-formatted files
countFastq-method	Sampling and streaming records from fastq files
countFastq-method	Read, write, and count records in FASTQ-formatted files
countLines	Count lines in all (text) files in a directory whose file name matches a pattern
coverage-method	(Legacy) "AlignedRead" class for aligned short reads

-- D --

dataPath	(Legacy) Accessors for ShortRead classes
defunct	Deprecated and defunct functions
deprecated	Deprecated and defunct functions
detail-method	(Legacy) "AlignedRead" class for aligned short reads
detail-method	(Legacy) "ExperimentPath" class representing a file hierarchy of data files
detail-method	Quality scores for short reads and their alignments
detail-method	(Legacy) "RochePath" class representing a Roche (454) experiment location
detail-method	(Legacy) 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	(Legacy) "SolexaPath" class representing a standard output file hierarchy
detail-method	(Legacy) "SolexaSet" coordinating Solexa output locations with sample annotations
dim-method	(Legacy) "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities
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 --

encoding-method	Quality scores for short reads and their alignments
ExperimentPath	(Legacy) "ExperimentPath" class representing a file hierarchy of data files
experimentPath	(Legacy) Accessors for ShortRead classes
ExperimentPath-class	(Legacy) "ExperimentPath" class representing a file hierarchy of data files
experimentPath-method	(Legacy) A base class for Roche experiment-wide data

-- F --

fac	Class '"Snapshot"'
fac-method	Class '"Snapshot"'
FastqFile	Sampling and streaming records from fastq files
FastqFile-class	Sampling and streaming records from fastq files
FastqFileList	Sampling and streaming records from fastq files
FastqFileList-class	Sampling and streaming records from fastq files
FastqFileList-method	Sampling and streaming records from fastq files
FastqFileReader-class	Sampling and streaming records from fastq files
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 and streaming records from fastq files
FastqSampler-class	Sampling and streaming records from fastq files
FastqSamplerList	Sampling and streaming records from fastq files
FastqSamplerList-class	Sampling and streaming records from fastq files
FastqSamplerList-method	Sampling and streaming records from fastq files
FastqStreamer	Sampling and streaming records from fastq files
FastqStreamer-class	Sampling and streaming records from fastq files
FastqStreamer-method	Sampling and streaming records from fastq files
FastqStreamerList	Sampling and streaming records from fastq files
FastqStreamerList-class	Sampling and streaming records from fastq files
FastqStreamerList-method	Sampling and streaming records from fastq files
files	Class '"Snapshot"'
files-method	Class '"Snapshot"'
filterFastq	Filter fastq from one file to another
flag	(Updated) quality assessment reports on short reads
flag-method	(Updated) quality assessment reports on short reads
functions	Class '"Snapshot"'
functions-method	Class '"Snapshot"'

-- G --

getTrellis	Class '"Snapshot"'
getTrellis-method	Class '"Snapshot"'

-- I --

id	"ShortRead" class for short reads
id-method	"ShortRead" class for short reads
idFilter	Functions for user-created and built-in ShortRead filters
ignore.strand	Class '"Snapshot"'
ignore.strand-method	Class '"Snapshot"'
imageAnalysisPath	(Legacy) Accessors for ShortRead classes
IntegerQuality	Construct objects indicating read or alignment quality
IntegerQuality-class	Quality scores for short reads and their alignments
intensity	(Legacy) "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities
Intensity-class	(Legacy) "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities
IntensityInfo-class	(Legacy) "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities
IntensityMeasure-class	(Legacy) "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities

-- L --

laneDescription	(Legacy) Accessors for ShortRead classes
laneNames	(Legacy) Accessors for ShortRead classes
laneNames-method	(Legacy) "SolexaSet" coordinating Solexa output locations with sample annotations
lapply-method	".SRUtil" and related classes
left	Class "SpTrellis"
left-method	Class "SpTrellis"
length-method	Quality scores for short reads and their alignments
length-method	".SRUtil" and related classes
length-method	"ShortRead" class for short reads
limits	Class "SnapshotFunction"
Logic-method	"SRFilterResult" for SRFilter output and statistics

-- M --

MAQMapQA	(Legacy) Quality assessment summaries from MAQ map files
MAQMapQA-class	(Legacy) 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	(Legacy) "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities

-- N --

name	"SRFilter" for representing functions operating on ShortRead objects
name-method	"SRFilter" for representing functions operating on ShortRead objects
name-method	"SRFilterResult" for SRFilter output and statistics
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
open.ShortReadFile	Sampling and streaming records from fastq files

-- P --

pan	Class '"Snapshot"'
pan-method	Class '"Snapshot"'
phenoData-method	(Legacy) A base class for Roche experiment-wide data
polyn	Utilities for common, simple operations
polynFilter	Functions for user-created and built-in ShortRead filters
position	(Legacy) Accessors for ShortRead classes
position-method	(Legacy) "AlignedRead" class for aligned short reads
positionFilter	Functions for user-created and built-in ShortRead filters

-- Q --

QA	(Updated) quality assessment reports on short reads
qa	Perform quality assessment on short reads
QA-class	(Updated) classes for representing quality assessment results
qa-method	"ShortReadQ" class for short reads and their quality scores
qa-method	(Legacy) "SolexaPath" class representing a standard output file hierarchy
qa-method	Perform quality assessment on short reads
qa2	(Updated) quality assessment reports on short reads
qa2-method	(Updated) quality assessment reports on short reads
QAAdapterContamination	(Updated) quality assessment reports on short reads
QAAdapterContamination-class	(Updated) classes for representing quality assessment results
QACollate	(Updated) quality assessment reports on short reads
QACollate-class	(Updated) classes for representing quality assessment results
QACollate-method	(Updated) quality assessment reports on short reads
QAData	(Updated) quality assessment reports on short reads
QAData-class	(Updated) classes for representing quality assessment results
QAFastqSource	(Updated) quality assessment reports on short reads
QAFastqSource-class	(Updated) classes for representing quality assessment results
QAFiltered	(Updated) quality assessment reports on short reads
QAFiltered-class	(Updated) classes for representing quality assessment results
QAFlagged	(Updated) quality assessment reports on short reads
QAFlagged-class	(Updated) classes for representing quality assessment results
QAFrequentSequence	(Updated) quality assessment reports on short reads
QAFrequentSequence-class	(Updated) classes for representing quality assessment results
QANucleotideByCycle	(Updated) quality assessment reports on short reads
QANucleotideByCycle-class	(Updated) classes for representing quality assessment results
QANucleotideUse	(Updated) quality assessment reports on short reads
QANucleotideUse-class	(Updated) classes for representing quality assessment results
QAQualityByCycle	(Updated) quality assessment reports on short reads
QAQualityByCycle-class	(Updated) classes for representing quality assessment results
QAQualityUse	(Updated) quality assessment reports on short reads
QAQualityUse-class	(Updated) classes for representing quality assessment results
QAReadQuality	(Updated) quality assessment reports on short reads
QAReadQuality-class	(Updated) classes for representing quality assessment results
QASequenceUse	(Updated) quality assessment reports on short reads
QASequenceUse-class	(Updated) classes for representing quality assessment results
QASource-class	(Updated) classes for representing quality assessment results
QASummary-class	(Updated) classes for representing quality assessment results
QualityScore-class	Quality scores for short reads and their alignments
qualPath	(Legacy) "RochePath" class representing a Roche (454) experiment location

-- R --

rbind-method	Virtual class for representing quality assessment results
rbind-method	(Updated) quality assessment reports on short reads
read454	(Legacy) "RochePath" class representing a Roche (454) experiment location
read454-method	(Legacy) "RochePath" class representing a Roche (454) experiment location
readAligned	(Legacy) Read aligned reads and their quality scores into R representations
readAligned-method	(Legacy) "SolexaPath" class representing a standard output file hierarchy
readAligned-method	(Legacy) "SolexaSet" coordinating Solexa output locations with sample annotations
readAligned-method	Deprecated and defunct functions
readAligned-method	(Legacy) Read aligned reads and their quality scores into R representations
readBaseQuality	(Legacy) Read short reads and their quality scores into R representations
readBaseQuality-method	(Legacy) "RochePath" class representing a Roche (454) experiment location
readBaseQuality-method	(Legacy) "SolexaPath" class representing a standard output file hierarchy
readBaseQuality-method	(Legacy) Read short reads and their quality scores into R representations
readBfaToc	(Legacy) Get a list of the sequences in a Maq .bfa file
readCount	(Legacy) A base class for Roche experiment-wide data
readData	(Legacy) A base class for Roche experiment-wide data
reader	Class "SnapshotFunction"
readFasta	Read and write FASTA files to or from ShortRead objects
readFasta-method	(Legacy) "RochePath" class representing a Roche (454) experiment location
readFasta-method	(Legacy) "SolexaPath" class representing a standard output file hierarchy
readFasta-method	Read and write FASTA files to or from ShortRead objects
readFastaQual	(Legacy) "RochePath" class representing a Roche (454) experiment location
readFastaQual-method	(Legacy) "RochePath" class representing a Roche (454) experiment location
readFastq	Read, write, and count records in FASTQ-formatted files
readFastq-method	Sampling and streaming records from fastq files
readFastq-method	(Legacy) "SolexaPath" class representing a standard output file hierarchy
readFastq-method	Read, write, and count records in FASTQ-formatted files
readIndex	(Legacy) A base class for Roche experiment-wide data
readIntensities	(Legacy) Read Illumina image intensity files
readIntensities-method	(Legacy) "SolexaPath" class representing a standard output file hierarchy
readIntensities-method	(Legacy) Read Illumina image intensity files
readIntensityInfo	(Legacy) "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities
readPath	(Legacy) "RochePath" class representing a Roche (454) experiment location
readPrb	(Legacy) Read Solexa prb files as fastq-style quality scores
readPrb-method	(Legacy) "SolexaPath" class representing a standard output file hierarchy
readPrb-method	(Legacy) Read Solexa prb files as fastq-style quality scores
readQseq	(Legacy) Read Solexa qseq files as fastq-style quality scores
readQseq-method	(Legacy) "SolexaPath" class representing a standard output file hierarchy
readQseq-method	(Legacy) Read Solexa qseq files as fastq-style quality scores
readQual	(Legacy) "RochePath" class representing a Roche (454) experiment location
readQual-method	(Legacy) "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	(Legacy) Quality assessment summaries from Bowtie files
report-method	Quality assessment of fastq files and ShortReadQ objects
report-method	(Legacy) Quality assessment summaries from MAQ map files
report-method	(Legacy) Quality assessment summaries from Solexa export and realign files
report-method	(Legacy) "SolexaPath" class representing a standard output file hierarchy
report-method	(Updated) quality assessment reports on short reads
report-method	Summarize quality assessment results into a report
report_html	Summarize quality assessment results into a report
report_html-method	(Legacy) Quality assessment summaries from Bowtie files
report_html-method	Quality assessment of fastq files and ShortReadQ objects
report_html-method	(Legacy) Quality assessment summaries from MAQ map files
report_html-method	(Legacy) Quality assessment summaries from Solexa export and realign files
restore	Class "SpTrellis"
restore-method	Class "SpTrellis"
reverse-method	Quality scores for short reads and their alignments
reverse-method	"ShortReadQ" class for short reads and their quality scores
reverseComplement-method	"ShortReadQ" class for short reads and their quality scores
right	Class "SpTrellis"
right-method	Class "SpTrellis"
RochePath	(Legacy) "RochePath" class representing a Roche (454) experiment location
RochePath-class	(Legacy) "RochePath" class representing a Roche (454) experiment location
RocheSet	(Legacy) Roche (454) experiment-wide data container
RocheSet-class	(Legacy) Roche (454) experiment-wide data container
RocheSet-method	(Legacy) "RochePath" class representing a Roche (454) experiment location
RtaIntensity	(Legacy) Construct objects of class "RtaIntensity"
RtaIntensity-class	(Legacy) Class "RtaIntensity"
runNames	(Legacy) "RochePath" class representing a Roche (454) experiment location
runNames-method	(Legacy) "RochePath" class representing a Roche (454) experiment location

-- S --

sapply-method	".SRUtil" and related classes
scanPath	(Legacy) 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
ShortReadFile-class	Sampling and streaming records from fastq files
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	(Legacy) "AlignedRead" class for aligned short reads
show-method	(Legacy) "ExperimentPath" class representing a file hierarchy of data files
show-method	(Legacy) "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities
show-method	Quality scores for short reads and their alignments
show-method	(Legacy) "RochePath" class representing a Roche (454) experiment location
show-method	"SRFilter" for representing functions operating on ShortRead objects
show-method	"SRFilterResult" for SRFilter output and statistics
show-method	(Legacy) A base class for Roche experiment-wide data
show-method	".SRUtil" and related classes
show-method	"ShortRead" class for short reads
show-method	FASTQ input and manipulation.
show-method	Class '"Snapshot"'
show-method	Class "SnapshotFunction"
show-method	(Legacy) Quality assessment summaries from Solexa export and realign files
show-method	(Legacy) "SolexaPath" class representing a standard output file hierarchy
show-method	(Legacy) "SolexaSet" coordinating Solexa output locations with sample annotations
show-method	Class "SpTrellis"
show-method	Virtual class for representing quality assessment results
show-method	(Updated) quality assessment reports on short reads
Snapshot	Class '"Snapshot"'
Snapshot-class	Class '"Snapshot"'
Snapshot-method	Class '"Snapshot"'
SnapshotFunction	Class "SnapshotFunction"
SnapshotFunction-class	Class "SnapshotFunction"
SnapshotFunctionList	Class "SnapshotFunction"
SnapshotFunctionList-class	Class "SnapshotFunction"
SnapshotFunctionList-method	Class "SnapshotFunction"
SolexaExportQA	(Legacy) Quality assessment summaries from Solexa export and realign files
SolexaExportQA-class	(Legacy) Quality assessment summaries from Solexa export and realign files
SolexaIntensity	(Legacy) Construct objects of class "SolexaIntensity" and "SolexaIntensityInfo"
SolexaIntensity-class	Classes "SolexaIntensity" and "SolexaIntensityInfo"
SolexaIntensityInfo	(Legacy) Construct objects of class "SolexaIntensity" and "SolexaIntensityInfo"
SolexaIntensityInfo-class	Classes "SolexaIntensity" and "SolexaIntensityInfo"
SolexaPath	(Legacy) "SolexaPath" class representing a standard output file hierarchy
solexaPath	(Legacy) Accessors for ShortRead classes
SolexaPath-class	(Legacy) "SolexaPath" class representing a standard output file hierarchy
SolexaRealignQA-class	(Legacy) Quality assessment summaries from Solexa export and realign files
SolexaSet	(Legacy) "SolexaSet" coordinating Solexa output locations with sample annotations
SolexaSet-class	(Legacy) "SolexaSet" coordinating Solexa output locations with sample annotations
SolexaSet-method	(Legacy) "SolexaPath" class representing a standard output file hierarchy
SolexaSet-method	(Legacy) "SolexaSet" coordinating Solexa output locations with sample annotations
sourcePath	(Legacy) A base class for Roche experiment-wide data
SpTrellis	Class "SpTrellis"
SpTrellis-class	Class "SpTrellis"
spViewPerFeature	Tools to visualize genomic data
srapply	Deprecated and defunct functions
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	(Legacy) "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	"ShortRead" class for short reads
sread-method	"ShortRead" class for short reads
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
SRFilterResult	"SRFilterResult" for SRFilter output and statistics
SRFilterResult-class	"SRFilterResult" for SRFilter output and statistics
SRList	".SRUtil" and related classes
srlist	".SRUtil" and related classes
SRList-class	".SRUtil" and related classes
srorder	Order, sort, and find duplicates in XStringSet objects
srorder-method	(Legacy) "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	(Legacy) "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	(Legacy) 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
stats	"SRFilterResult" for SRFilter output and statistics
stats-method	"SRFilterResult" for SRFilter output and statistics
strand-method	(Legacy) "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
togglefun	Class '"Snapshot"'
togglefun-method	Class '"Snapshot"'
togglep	Class '"Snapshot"'
togglep-method	Class '"Snapshot"'
togglez	Class '"Snapshot"'
togglez-method	Class '"Snapshot"'
trellis-class	Class '"Snapshot"'
trimEnds	Trim ends of reads based on nucleotides or qualities
trimEnds-method	Trim ends of reads based on nucleotides or qualities
trimLRPatterns-method	"ShortRead" class for short reads
trimTails	Trim ends of reads based on nucleotides or qualities
trimTails-method	Quality scores for short reads and their alignments
trimTails-method	"ShortReadQ" class for short reads and their quality scores
trimTails-method	Trim ends of reads based on nucleotides or qualities
trimTailw	Trim ends of reads based on nucleotides or qualities
trimTailw-method	Quality scores for short reads and their alignments
trimTailw-method	"ShortReadQ" class for short reads and their quality scores
trimTailw-method	Trim ends of reads based on nucleotides or qualities

-- U --

uniqueFilter

Deprecated functions from the ShortRead package

-- V --

vclass	(Legacy) Accessors for ShortRead classes
view	Class '"Snapshot"'
view-method	Class '"Snapshot"'
viewer	Class "SnapshotFunction"
vrange	Class '"Snapshot"'
vrange-method	Class '"Snapshot"'

-- 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
writeFasta-method	Read and write FASTA files to or from ShortRead objects
writeFastq	Read, write, and count records in FASTQ-formatted files
writeFastq-method	"ShortReadQ" class for short reads and their quality scores

-- Y --

yield	Sampling and streaming records from fastq files
yield-method	Sampling and streaming records from fastq files

-- Z --

zi	Class "SpTrellis"
zi-method	Class "SpTrellis"
zo	Class "SpTrellis"
zo-method	Class "SpTrellis"
zoom	Class '"Snapshot"'
zoom-method	Class '"Snapshot"'

-- misc --

!-method	"SRFilterResult" for SRFilter output and statistics
%in%-method	(Legacy) "AlignedRead" class for aligned short reads
.QA-class	Virtual class for representing quality assessment results
.QA2-class	(Updated) classes for representing quality assessment results
.Roche-class	FASTQ input and manipulation.
.ShortReadBase-class	FASTQ input and manipulation.
.Solexa-class	FASTQ input and manipulation.
.SRUtil-class	".SRUtil" and related classes
[-method	(Legacy) "AlignedRead" class for aligned short reads
[-method	(Legacy) "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities
[-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	"ShortReadQ" class for short reads and their quality scores
[[-method	(Legacy) "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities
[[-method	Quality scores for short reads and their alignments
[[-method	".SRUtil" and related classes