ShortReadBase-package	ShortRead-package
%in%,AlignedRead,RangesList-method	AlignedRead-class
.QA-class	QA-class
.Roche-class	ShortRead-package
.ShortReadBase-class	ShortRead-package
.Solexa-class	ShortRead-package
.SRUtil-class	SRUtil-class
accessors	accessors
alignData	accessors
alignDataFilter	srFilter
AlignedDataFrame	AlignedDataFrame
AlignedDataFrame-class	AlignedDataFrame-class
AlignedRead	AlignedRead
AlignedRead-class	AlignedRead-class
alignQuality	accessors
alignQualityFilter	srFilter
alphabet,FastqQuality-method	QualityScore-class
alphabetByCycle	alphabetByCycle
alphabetByCycle,BStringSet-method	alphabetByCycle
alphabetByCycle,FastqQuality-method	QualityScore-class
alphabetByCycle,ShortRead-method	ShortRead-class
alphabetByCycle,ShortReadQ-method	ShortReadQ-class
alphabetFrequency,FastqQuality-method	QualityScore-class
alphabetScore	alphabetScore
alphabetScore,FastqQuality-method	QualityScore-class
alphabetScore,SFastqQuality-method	QualityScore-class
alphabetScore,ShortReadQ-method	ShortReadQ-class
analysisPath	accessors
append,.ShortReadBase,.ShortReadBase,ANY-method	ShortRead-package
append,AlignedDataFrame,AlignedDataFrame,missing-method	AlignedDataFrame-class
append,AlignedRead,AlignedRead,missing-method	AlignedRead-class
append,MatrixQuality,MatrixQuality,missing-method	QualityScore-class
append,QualityScore,QualityScore,missing-method	QualityScore-class
append,ShortRead,ShortRead,missing-method	ShortRead-class
append,ShortReadQ,ShortReadQ,missing-method	ShortReadQ-class
ArrayIntensity	Intensity-class
ArrayIntensity-class	Intensity-class
baseCallPath	accessors
basePath	deprecated
BowtieQA-class	BowtieQA-class
chromosome	accessors
chromosome,AlignedRead-method	AlignedRead-class
chromosomeFilter	srFilter
clean	clean
clean,DNAStringSet-method	clean
clean,ShortRead-method	ShortRead-class
coerce,AlignedRead,RangesList-method	AlignedRead-class
coerce,FastqQuality,matrix-method	QualityScore-class
coerce,FastqQuality,numeric-method	QualityScore-class
coerce,FastqQuality,PhredQuality-method	QualityScore-class
coerce,PairwiseAlignedXStringSet,AlignedRead-method	AlignedRead-class
coerce,SFastqQuality,matrix-method	QualityScore-class
coerce,SFastqQuality,SolexaQuality-method	QualityScore-class
coerce,ShortReadQ,QualityScaledDNAStringSet-method	ShortReadQ-class
compact,FastqQuality-method	QualityScore-class
compact,ShortRead-method	ShortRead-class
compact,ShortReadQ-method	ShortReadQ-class
compose	srFilter
countLines	countLines
coverage,AlignedRead-method	AlignedRead-class
dataPath	accessors
deprecated	deprecated
detail	detail
detail,.ShortReadBase-method	SRUtil-class
detail,AlignedRead-method	AlignedRead-class
detail,ExperimentPath-method	ExperimentPath-class
detail,QualityScore-method	QualityScore-class
detail,RochePath-method	RochePath-class
detail,ShortRead-method	ShortRead-class
detail,ShortReadQ-method	ShortReadQ-class
detail,SolexaPath-method	SolexaPath-class
detail,SolexaSet-method	SolexaSet-class
detail,SRList-method	SRUtil-class
detail,SRSet-method	SRSet-class
detail,SRVector-method	SRUtil-class
dim,Intensity-method	Intensity-class
dim,MatrixQuality-method	QualityScore-class
dustyFilter	srFilter
dustyScore	dustyScore
dustyScore,DNAStringSet-method	dustyScore
dustyScore,ShortRead-method	dustyScore
ExperimentPath	ExperimentPath-class
experimentPath	accessors
experimentPath,SRSet-method	SRSet-class
ExperimentPath-class	ExperimentPath-class
FastqQA	FastqQA-class
FastqQA-class	FastqQA-class
FastqQuality	QualityScore
FastqQuality,BStringSet-method	QualityScore
FastqQuality,character-method	QualityScore
FastqQuality,missing-method	QualityScore
FastqQuality-class	QualityScore-class
id	accessors
id,ShortRead-method	ShortRead-class
idFilter	srFilter
imageAnalysisPath	accessors
IntegerQuality	QualityScore
IntegerQuality-class	QualityScore-class
intensity	Intensity-class
Intensity-class	Intensity-class
IntensityInfo-class	Intensity-class
IntensityMeasure-class	Intensity-class
laneDescription	accessors
laneNames	accessors
laneNames,AnnotatedDataFrame-method	SolexaSet-class
laneNames,SolexaSet-method	SolexaSet-class
lapply,SRList,ANY-method	SRUtil-class
lapply,SRList-method	SRUtil-class
length,MatrixQuality-method	QualityScore-class
length,QualityScore-method	QualityScore-class
length,ShortRead-method	ShortRead-class
length,SRList-method	SRUtil-class
MAQMapQA	MAQMapQA-class
MAQMapQA-class	MAQMapQA-class
MatrixQuality	QualityScore
MatrixQuality-class	QualityScore-class
measurementError	Intensity-class
name	SRFilter-class
name,SRFilter-method	SRFilter-class
names,SRList-method	SRUtil-class
names<-,SRList,character-method	SRUtil-class
narrow,FastqQuality-method	QualityScore-class
narrow,MatrixQuality-method	QualityScore-class
narrow,ShortRead-method	ShortRead-class
narrow,ShortReadQ-method	ShortReadQ-class
nFilter	srFilter
NumericQuality	QualityScore
NumericQuality-class	QualityScore-class
phenoData,SRSet-method	SRSet-class
pileup	deprecated
polyn	polyn
polynFilter	srFilter
position	accessors
position,AlignedRead-method	AlignedRead-class
positionFilter	srFilter
qa	qa
qa,character-method	qa
qa,list-method	qa
qa,ShortReadQ-method	ShortReadQ-class
qa,SolexaPath-method	SolexaPath-class
QualityScore-class	QualityScore-class
qualPath	RochePath-class
rbind,.QA-method	QA-class
read454	RochePath-class
read454,RochePath-method	RochePath-class
readAligned	readAligned
readAligned,character-method	readAligned
readAligned,SolexaPath-method	SolexaPath-class
readAligned,SolexaSet-method	SolexaSet-class
readBaseQuality	readBaseQuality
readBaseQuality,character-method	readBaseQuality
readBaseQuality,RochePath-method	RochePath-class
readBaseQuality,SolexaPath-method	SolexaPath-class
readBfaToc	readBfaToc
readCount	SRSet-class
readData	SRSet-class
readFasta	RochePath-class
readFasta,character-method	RochePath-class
readFasta,RochePath-method	RochePath-class
readFastaQual	RochePath-class
readFastaQual,character-method	RochePath-class
readFastaQual,RochePath-method	RochePath-class
readFastq	readFastq
readFastq,character-method	readFastq
readFastq,SolexaPath-method	SolexaPath-class
readIndex	SRSet-class
readInfo	Intensity-class
readIntensities	readIntensities
readIntensities,character-method	readIntensities
readIntensities,SolexaPath-method	SolexaPath-class
readPath	RochePath-class
readPrb	readPrb
readPrb,character-method	readPrb
readPrb,SolexaPath-method	SolexaPath-class
readQseq	readQseq
readQseq,character-method	readQseq
readQseq,SolexaPath-method	SolexaPath-class
readQual	RochePath-class
readQual,character-method	RochePath-class
readQual,RochePath-method	RochePath-class
readXStringColumns	readXStringColumns
report	report
report,ANY-method	report
report,BowtieQA-method	BowtieQA-class
report,FastqQA-method	FastqQA-class
report,MAQMapQA-method	MAQMapQA-class
report,SolexaExportQA-method	SolexaExportQA-class
report,SolexaPath-method	SolexaPath-class
RochePath	RochePath-class
RochePath-class	RochePath-class
RocheSet	RocheSet-class
RocheSet,character-method	RochePath-class
RocheSet,RochePath-method	RochePath-class
RocheSet-class	RocheSet-class
runNames	RochePath-class
runNames,RochePath-method	RochePath-class
sapply,SRList-method	SRUtil-class
scanPath	accessors
SFastqQuality	QualityScore
SFastqQuality,BStringSet-method	QualityScore
SFastqQuality,character-method	QualityScore
SFastqQuality,missing-method	QualityScore
SFastqQuality-class	QualityScore-class
ShortRead	ShortRead-class
ShortRead,DNAStringSet,BStringSet-method	ShortRead-class
ShortRead,DNAStringSet,missing-method	ShortRead-class
ShortRead,missing,missing-method	ShortRead-class
ShortRead-class	ShortRead-class
ShortReadQ	ShortReadQ-class
ShortReadQ,DNAStringSet,QualityScore,BStringSet-method	ShortReadQ-class
ShortReadQ,DNAStringSet,QualityScore,missing-method	ShortReadQ-class
ShortReadQ,missing,missing,missing-method	ShortReadQ-class
ShortReadQ-class	ShortReadQ-class
ShortReadQQA-class	FastqQA-class
show,.QA-method	QA-class
show,.ShortReadBase-method	ShortRead-package
show,AlignedRead-method	AlignedRead-class
show,ExperimentPath-method	ExperimentPath-class
show,FastqQuality-method	QualityScore-class
show,Intensity-method	Intensity-class
show,IntensityMeasure-method	Intensity-class
show,NumericQuality-method	QualityScore-class
show,RochePath-method	RochePath-class
show,ShortRead-method	ShortRead-class
show,SolexaExportQA-method	SolexaExportQA-class
show,SolexaPath-method	SolexaPath-class
show,SolexaSet-method	SolexaSet-class
show,SRFilter-method	SRFilter-class
show,SRList-method	SRUtil-class
show,SRSet-method	SRSet-class
show,SRVector-method	SRUtil-class
SolexaExportQA	SolexaExportQA-class
SolexaExportQA-class	SolexaExportQA-class
SolexaIntensity	SolexaIntensity
SolexaIntensity-class	SolexaIntensity-class
SolexaIntensityInfo	SolexaIntensity
SolexaIntensityInfo-class	SolexaIntensity-class
SolexaPath	SolexaPath-class
solexaPath	accessors
SolexaPath-class	SolexaPath-class
SolexaRealignQA-class	SolexaExportQA-class
SolexaSet	SolexaSet-class
SolexaSet,character-method	SolexaSet-class
SolexaSet,SolexaPath-method	SolexaPath-class
SolexaSet-class	SolexaSet-class
sourcePath	SRSet-class
srapply	srapply
srdistance	srdistance
srdistance,DNAStringSet,character-method	srdistance
srdistance,DNAStringSet,DNAString-method	srdistance
srdistance,DNAStringSet,DNAStringSet-method	srdistance
srdistance,ShortRead,ANY-method	ShortRead-class
srdistanceFilter	srFilter
srduplicated	srduplicated
srduplicated,AlignedRead-method	AlignedRead-class
srduplicated,FastqQuality-method	QualityScore-class
srduplicated,ShortRead-method	ShortRead-class
srduplicated,XStringSet-method	srduplicated
sread	accessors
SRError	SRUtil-class
SRError-class	SRUtil-class
srFilter	srFilter
srFilter,function-method	srFilter
srFilter,missing-method	srFilter
srFilter,SRFilter-method	SRFilter-class
SRFilter-class	SRFilter-class
SRList	SRUtil-class
SRList-class	SRUtil-class
srorder	srduplicated
srorder,AlignedRead-method	AlignedRead-class
srorder,FastqQuality-method	QualityScore-class
srorder,ShortRead-method	ShortRead-class
srorder,XStringSet-method	srduplicated
srrank	srduplicated
srrank,AlignedRead-method	AlignedRead-class
srrank,FastqQuality-method	QualityScore-class
srrank,ShortRead-method	ShortRead-class
srrank,XStringSet-method	srduplicated
SRSet-class	SRSet-class
srsort	srduplicated
srsort,FastqQuality-method	QualityScore-class
srsort,ShortRead-method	ShortRead-class
srsort,XStringSet-method	srduplicated
SRVector	SRUtil-class
SRVector-class	SRUtil-class
SRWarn	SRUtil-class
SRWarn-class	SRUtil-class
strand,AlignedRead-method	AlignedRead-class
strandFilter	srFilter
tables	tables
tables,ShortRead-method	ShortRead-class
tables,XStringSet-method	tables
trimLRPatterns,ShortRead-method	ShortRead-class
uniqueFilter	srFilter
vclass	accessors
width,FastqQuality-method	QualityScore-class
width,MatrixQuality-method	QualityScore-class
width,NumericQuality-method	QualityScore-class
width,QualityScore-method	QualityScore-class
width,ShortRead-method	ShortRead-class
writeFastq	readFastq
writeFastq,ShortReadQ-method	ShortReadQ-class
[,AlignedRead,ANY,ANY,ANY-method	AlignedRead-class
[,AlignedRead,ANY,ANY-method	AlignedRead-class
[,AlignedRead,ANY,missing,ANY-method	AlignedRead-class
[,AlignedRead,ANY,missing-method	AlignedRead-class
[,AlignedRead,missing,ANY,ANY-method	AlignedRead-class
[,AlignedRead,missing,ANY-method	AlignedRead-class
[,AlignedRead,missing,missing,ANY-method	AlignedRead-class
[,AlignedRead,missing,missing-method	AlignedRead-class
[,IntensityMeasure,ANY,ANY,ANY-method	Intensity-class
[,IntensityMeasure,ANY,ANY-method	Intensity-class
[,IntensityMeasure,ANY,missing,ANY-method	Intensity-class
[,IntensityMeasure,missing,ANY,ANY-method	Intensity-class
[,IntensityMeasure,missing,missing,ANY-method	Intensity-class
[,MatrixQuality,ANY,missing,ANY-method	QualityScore-class
[,MatrixQuality,ANY,missing-method	QualityScore-class
[,QualityScore,ANY,missing,ANY-method	QualityScore-class
[,QualityScore,ANY,missing-method	QualityScore-class
[,ShortRead,ANY,ANY,ANY-method	ShortRead-class
[,ShortRead,ANY,ANY-method	ShortRead-class
[,ShortRead,ANY,missing,ANY-method	ShortRead-class
[,ShortRead,ANY,missing-method	ShortRead-class
[,ShortRead,missing,ANY,ANY-method	ShortRead-class
[,ShortRead,missing,ANY-method	ShortRead-class
[,ShortRead,missing,missing,ANY-method	ShortRead-class
[,ShortRead,missing,missing-method	ShortRead-class
[,ShortReadQ,ANY,ANY,ANY-method	ShortReadQ-class
[,ShortReadQ,ANY,ANY-method	ShortReadQ-class
[,ShortReadQ,ANY,missing,ANY-method	ShortReadQ-class
[,ShortReadQ,ANY,missing-method	ShortReadQ-class
[,ShortReadQ,missing,ANY,ANY-method	ShortReadQ-class
[,ShortReadQ,missing,ANY-method	ShortReadQ-class
[,ShortReadQ,missing,missing,ANY-method	ShortReadQ-class
[,ShortReadQ,missing,missing-method	ShortReadQ-class
[,SolexaIntensity,ANY,ANY,ANY-method	SolexaIntensity-class
[,SolexaIntensity,ANY,ANY-method	SolexaIntensity-class
[,SolexaIntensity,ANY,missing,ANY-method	SolexaIntensity-class
[,SolexaIntensity,missing,ANY,ANY-method	SolexaIntensity-class
[,SolexaIntensity,missing,missing,ANY-method	SolexaIntensity-class
[,SRList,ANY,missing,ANY-method	SRUtil-class
[,SRList,ANY,missing-method	SRUtil-class
[[,ArrayIntensity,ANY,ANY-method	Intensity-class
[[,MatrixQuality,ANY,missing-method	QualityScore-class
[[,QualityScore,ANY,missing-method	QualityScore-class
[[,SRList,ANY,missing-method	SRUtil-class
