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 |
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 |
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 |
[,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 |