R453Plus1Toolbox
A package for importing and analyzing data from Roche's Genome Sequencer System

Package index
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Vignettes
Functions
416
Source code
39
Man pages
64
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R453Plus1Toolbox: A package for importing and analyzing data from Roche's Genome Sequencer System
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API

API for R453Plus1Toolbox
A package for importing and analyzing data from Roche's Genome Sequencer System

Global functions
.addComma Source code
.alignShortReads_AVASet Source code
.alignShortReads_DNAStringSet Source code
.annotateReference Source code
.annotateVariantBlock Source code
.annotateVariants_AVASet Source code
.annotateVariants_MapperSet Source code
.annotateVariants_data.frame Source code
.annotatedVariants_to_dataFrame Source code
.ava2vcf Source code
.baseFrequency Source code
.baseFrequency_sff Source code
.baseFrequency_sr Source code
.baseQualityHist Source code
.baseQualityHist_sff Source code
.baseQualityHist_sr Source code
.baseQualityStats Source code
.baseQualityStats_sff Source code
.baseQualityStats_sr Source code
.calculateTiTv Source code
.catchBadInput Source code
.codingRegion Source code
.complementStrand Source code
.complexity.dust Source code
.complexity.dust_sff Source code
.complexity.dust_sr Source code
.complexity.entropy Source code
.complexity.entropy_sff Source code
.complexity.entropy_sr Source code
.computeBPDistance_nsc Source code
.computeBPDistance_sc Source code
.computeLocalCoordinates Source code
.coverageOnTarget Source code
.createNavigation Source code
.demultiplexReads Source code
.detectBreakpoints Source code
.dinucleotideOddsRatio Source code
.dinucleotideOddsRatio_sff Source code
.dinucleotideOddsRatio_sr Source code
.filterChimericReads Source code
.flowgramBarplot Source code
.gcContent Source code
.gcContentHist Source code
.gcContentHist_sff Source code
.gcContentHist_sr Source code
.gcContent_sff Source code
.gcContent_sr Source code
.gcPerPosition Source code
.gcPerPosition_sff Source code
.gcPerPosition_sr Source code
.genomeSequencerMIDs Source code
.genomeSequencerMIDs_character Source code
.getAlignedReads Source code
.getEnsemblInfo Source code
.getMutations Source code
.getVariantPercentages Source code
.homopolymerHist Source code
.htmlReport Source code
.initHtmlReportAVASet Source code
.initHtmlReportGSMSet Source code
.initializePlot Source code
.markRelatedBreakpoints Source code
.mergeBreakpoints Source code
.nucleotideCharts Source code
.nucleotideCharts_sff Source code
.nucleotideCharts_sr Source code
.plotAmpliconCoverage Source code
.plotChimericReads Source code
.plotMutationsBasePairPlot Source code
.plotReads Source code
.plotReadsBasePairs Source code
.plotReference Source code
.plotReferenceBasePairs Source code
.plotVariants Source code
.plotVariationFrequency_data.frame Source code
.plotVariationFrequency_file Source code
.positionQualityBoxplot Source code
.positionQualityBoxplot_sff Source code
.positionQualityBoxplot_sr Source code
.qualityReport Source code
.read454BaseCallerMetrics_character Source code
.read454QualityFilterMetrics_character Source code
.readGSMAssayFeatureData Source code
.readGSMPhenoData Source code
.readLengthHist Source code
.readLengthHist_sff Source code
.readLengthHist_sr Source code
.readLengthStats Source code
.readLengthStats_sff Source code
.readLengthStats_sr Source code
.readsOnTarget Source code
.removeLinker Source code
.removeSoftclips Source code
.reverseC2 Source code
.sequenceCaptureLinkers Source code
.sequenceCaptureLinkers_character Source code
.sequenceQualityHist Source code
.sequenceQualityHist_sff Source code
.sequenceQualityHist_sr Source code
.setVariantFilter Source code
AVASet Man page
AVASet,character,character,missing,missing,missing,missing,missi Man page
AVASet,character,missing,character,character,character,character Man page
AVASet,character,missing,character,character,character,missing,m Man page
AVASet,character,missing,missing,missing,missing,missing,missing Man page
AVASet-class Man page
AnnotatedVariants-class Man page
Breakpoints-class Man page
MapperSet Man page
MapperSet,character-method Man page
MapperSet-class Man page
SFFContainer Man page
SFFContainer-class Man page
SFFRead Man page
SFFRead-class Man page
[,AVASet,ANY,ANY,ANY-method Man page
[,AVASet,ANY,ANY-method Man page
[,Breakpoints,ANY,ANY,ANY-method Man page
[,Breakpoints,ANY,ANY-method Man page
[,SFFContainer,ANY,ANY,ANY-method Man page
[,SFFContainer,ANY,ANY-method Man page
addRead Man page
addRead,SFFContainer,SFFRead-method Man page
alignShortReads Man page
alignShortReads,AVASet,BSgenome,character,logical-method Man page
alignShortReads,AVASet,BSgenome,character,missing-method Man page
alignShortReads,AVASet,BSgenome,missing,logical-method Man page
alignShortReads,AVASet,BSgenome,missing,missing-method Man page
alignShortReads,AVASet,DNAStringSet,character-method Man page
alignShortReads,DNAStringSet,BSgenome,character,logical-method Man page
alignShortReads,DNAStringSet,BSgenome,character,missing-method Man page
alignShortReads,DNAStringSet,BSgenome,missing,logical-method Man page
alignShortReads,DNAStringSet,BSgenome,missing,missing-method Man page
alignedReadsC1 Man page
alignedReadsC1,Breakpoints-method Man page
alignedReadsC1<- Man page
alignedReadsC1<-,Breakpoints,list-method Man page
alignedReadsC2 Man page
alignedReadsC2,Breakpoints-method Man page
alignedReadsC2<- Man page
alignedReadsC2<-,Breakpoints,list-method Man page
annotateVariants Man page
annotateVariants,AVASet,missing-method Man page
annotateVariants,AVASet-method Man page
annotateVariants,MapperSet,BSgenome-method Man page
annotateVariants,MapperSet,missing-method Man page
annotateVariants,MapperSet-method Man page
annotateVariants,data.frame,missing-method Man page
annotatedVariants Man page
annotatedVariants,AnnotatedVariants-method Man page
annotatedVariants<-,AnnotatedVariants,list-method Man page
assayDataAmp Man page
assayDataAmp,AVASet-method Man page
assayDataAmp<- Man page
assayDataAmp<-,AVASet,AssayData-method Man page
ava2vcf Man page
ava2vcf,AVASet-method Man page
avaSetExample Man page
avaSetFiltered Man page
avaSetFiltered_annot Man page
baseFrequency Man page
baseFrequency,DNAStringSet-method Man page
baseFrequency,SFFContainer-method Man page
baseFrequency,ShortRead-method Man page
baseQualityHist Man page
baseQualityHist,QualityScaledDNAStringSet-method Man page
baseQualityHist,SFFContainer-method Man page
baseQualityHist,ShortReadQ-method Man page
baseQualityStats Man page
baseQualityStats,QualityScaledDNAStringSet-method Man page
baseQualityStats,SFFContainer-method Man page
baseQualityStats,ShortReadQ-method Man page
breakpoints Man page
calculateTiTv Man page
calculateTiTv,AVASet-method Man page
calculateTiTv,MapperSet-method Man page
captureArray Man page
clipAdapterLeft Man page
clipAdapterLeft,SFFContainer-method Man page
clipAdapterLeft,SFFRead-method Man page
clipAdapterLeft<- Man page
clipAdapterLeft<-,SFFContainer,numeric-method Man page
clipAdapterLeft<-,SFFRead,numeric-method Man page
clipAdapterRight Man page
clipAdapterRight,SFFContainer-method Man page
clipAdapterRight,SFFRead-method Man page
clipAdapterRight<- Man page
clipAdapterRight<-,SFFContainer,numeric-method Man page
clipAdapterRight<-,SFFRead,numeric-method Man page
clipQualityLeft Man page
clipQualityLeft,SFFContainer-method Man page
clipQualityLeft,SFFRead-method Man page
clipQualityLeft<- Man page
clipQualityLeft<-,SFFContainer,numeric-method Man page
clipQualityLeft<-,SFFRead,numeric-method Man page
clipQualityRight Man page
clipQualityRight,SFFContainer-method Man page
clipQualityRight,SFFRead-method Man page
clipQualityRight<- Man page
clipQualityRight<-,SFFContainer,numeric-method Man page
clipQualityRight<-,SFFRead,numeric-method Man page
commonAlignC1 Man page
commonAlignC1,Breakpoints-method Man page
commonAlignC1<- Man page
commonAlignC1<-,Breakpoints,list-method Man page
commonAlignC2 Man page
commonAlignC2,Breakpoints-method Man page
commonAlignC2<- Man page
commonAlignC2<-,Breakpoints,list-method Man page
commonBpsC1 Man page
commonBpsC1,Breakpoints-method Man page
commonBpsC1<- Man page
commonBpsC1<-,Breakpoints,list-method Man page
commonBpsC2 Man page
commonBpsC2,Breakpoints-method Man page
commonBpsC2<- Man page
commonBpsC2<-,Breakpoints,list-method Man page
complexity.dust Man page
complexity.dust,DNAStringSet-method Man page
complexity.dust,SFFContainer-method Man page
complexity.dust,ShortRead-method Man page
complexity.entropy Man page
complexity.entropy,DNAStringSet-method Man page
complexity.entropy,SFFContainer-method Man page
complexity.entropy,ShortRead-method Man page
convertCigar Man page
coverageOnTarget Man page
coverageOnTarget,list,GRanges-method Man page
demultiplexReads Man page
demultiplexReads,XStringSet,XStringSet,missing,logical-method Man page
demultiplexReads,XStringSet,XStringSet,missing,missing-method Man page
demultiplexReads,XStringSet,XStringSet,numeric,logical-method Man page
demultiplexReads,XStringSet,XStringSet,numeric,missing-method Man page
detectBreakpoints Man page
detectBreakpoints,list-method Man page
dinucleotideOddsRatio Man page
dinucleotideOddsRatio,DNAStringSet-method Man page
dinucleotideOddsRatio,SFFContainer-method Man page
dinucleotideOddsRatio,ShortRead-method Man page
extendedCIGARToList Man page Source code
fDataAmp Man page
fDataAmp,AVASet-method Man page
featureDataAmp Man page
featureDataAmp,AVASet-method Man page
featureDataAmp<- Man page
featureDataAmp<-,AVASet,AnnotatedDataFrame-method Man page
filterChimericReads Man page
filterChimericReads,list,IntegerRangesList,DNAString,missing,mis Man page
filterChimericReads,list,IntegerRangesList,DNAString,numeric,num Man page
filterChimericReads,list,IntegerRangesList,missing,missing,missi Man page
filterChimericReads,list,IntegerRangesList,missing,numeric,numer Man page
filterChimericReads,list,missing,DNAString,missing,missing-metho Man page
filterChimericReads,list,missing,DNAString,numeric,numeric-metho Man page
filterChimericReads,list,missing,missing,missing,missing-method Man page
filterChimericReads,list,missing,missing,numeric,numeric-method Man page
flowChars Man page
flowChars,SFFContainer-method Man page
flowChars,SFFRead-method Man page
flowChars<- Man page
flowChars<-,SFFContainer,character-method Man page
flowChars<-,SFFRead,character-method Man page
flowIndexes Man page
flowIndexes,SFFContainer-method Man page
flowIndexes,SFFRead-method Man page
flowIndexes<- Man page
flowIndexes<-,SFFContainer,list-method Man page
flowIndexes<-,SFFRead,numeric-method Man page
flowgram Man page
flowgram,SFFRead-method Man page
flowgram<- Man page
flowgram<-,SFFRead,numeric-method Man page
flowgramBarplot Man page
flowgramBarplot,SFFRead-method Man page
flowgramFormat Man page
flowgramFormat,SFFContainer-method Man page
flowgramFormat,SFFRead-method Man page
flowgramFormat<- Man page
flowgramFormat<-,SFFContainer,numeric-method Man page
flowgramFormat<-,SFFRead,numeric-method Man page
flowgrams Man page
flowgrams,SFFContainer-method Man page
flowgrams<- Man page
flowgrams<-,SFFContainer,list-method Man page
gcContent Man page
gcContent,DNAStringSet-method Man page
gcContent,SFFContainer-method Man page
gcContent,ShortRead-method Man page
gcContentHist Man page
gcContentHist,DNAStringSet-method Man page
gcContentHist,SFFContainer-method Man page
gcContentHist,ShortRead-method Man page
gcPerPosition Man page
gcPerPosition,DNAStringSet-method Man page
gcPerPosition,SFFContainer-method Man page
gcPerPosition,ShortRead-method Man page
genomeSequencerMIDs Man page
genomeSequencerMIDs,character-method Man page
genomeSequencerMIDs,missing-method Man page
getAlignedReads Man page
getAlignedReads,AVASet-method Man page
getAminoAbbr Man page Source code
getRead Man page
getRead,SFFContainer,character-method Man page
getReadStatus Man page
getReadStatus,MapperSet-method Man page
getVariantPercentages Man page
getVariantPercentages,AVASet-method Man page
getVariantPercentages,MapperSet-method Man page
homopolymerHist Man page
homopolymerHist,SFFRead-method Man page
htmlReport Man page
htmlReport,AVASet-method Man page
htmlReport,MapperSet-method Man page
keySequence Man page
keySequence,SFFContainer-method Man page
keySequence,SFFRead-method Man page
keySequence<- Man page
keySequence<-,SFFContainer,character-method Man page
keySequence<-,SFFRead,character-method Man page
length,Breakpoints-method Man page
listToExtendedCIGAR Man page Source code
mapperSetExample Man page
mergeBreakpoints Man page
mergeBreakpoints,Breakpoints,missing,list-method Man page
mergeBreakpoints,Breakpoints,missing,missing-method Man page
mergeBreakpoints,Breakpoints,numeric,missing-method Man page
mutationInfo Man page
name Man page
name,SFFContainer-method Man page
name,SFFRead-method Man page
name<- Man page
name<-,SFFContainer,character-method Man page
name<-,SFFRead,character-method Man page
names,AnnotatedVariants-method Man page
names,Breakpoints-method Man page
names<-,AnnotatedVariants,character-method Man page
names<-,Breakpoints,ANY-method Man page
nucleotideCharts Man page
nucleotideCharts,DNAStringSet-method Man page
nucleotideCharts,SFFContainer-method Man page
nucleotideCharts,ShortRead-method Man page
plotAmpliconCoverage Man page
plotAmpliconCoverage,AVASet,character,logical-method Man page
plotAmpliconCoverage,AVASet,character,missing-method Man page
plotAmpliconCoverage,AVASet,missing,logical-method Man page
plotAmpliconCoverage,AVASet,missing,missing-method Man page
plotChimericReads Man page
plotChimericReads,Breakpoints-method Man page
plotVariants Man page
plotVariants,AnnotatedVariants,character-method Man page
plotVariants,data.frame,character-method Man page
plotVariationFrequency Man page
plotVariationFrequency,character,numeric-method Man page
positionQualityBoxplot Man page
positionQualityBoxplot,QualityScaledDNAStringSet-method Man page
positionQualityBoxplot,SFFContainer-method Man page
positionQualityBoxplot,ShortReadQ-method Man page
quality,SFFRead-method Man page
quality<- Man page
quality<-,SFFRead,BString-method Man page
qualityReportSFF Man page Source code
read Man page
read,SFFRead-method Man page
read<- Man page
read<-,SFFRead,QualityScaledDNAStringSet-method Man page
readLengthHist Man page
readLengthHist,DNAStringSet-method Man page
readLengthHist,SFFContainer-method Man page
readLengthHist,ShortRead-method Man page
readLengthStats Man page
readLengthStats,DNAStringSet-method Man page
readLengthStats,SFFContainer-method Man page
readLengthStats,ShortRead-method Man page
readSFF Man page Source code
reads Man page
reads,SFFContainer-method Man page
reads<- Man page
reads<-,SFFContainer,QualityScaledDNAStringSet-method Man page
readsOnTarget Man page
readsOnTarget,list,GRanges-method Man page
referenceSequences Man page
referenceSequences,AVASet-method Man page
referenceSequences<- Man page
referenceSequences<-,AVASet,AlignedRead-method Man page
regions Man page
removeLinker Man page
removeLinker,XStringSet,DNAString,logical,numeric,numeric-method Man page
removeLinker,XStringSet,DNAString,missing,missing,missing-method Man page
seqsC1 Man page
seqsC1,Breakpoints-method Man page
seqsC1<- Man page
seqsC1<-,Breakpoints,list-method Man page
seqsC2 Man page
seqsC2,Breakpoints-method Man page
seqsC2<- Man page
seqsC2<-,Breakpoints,list-method Man page
sequenceCaptureLinkers Man page
sequenceCaptureLinkers,character-method Man page
sequenceCaptureLinkers,missing-method Man page
sequenceQualityHist Man page
sequenceQualityHist,QualityScaledDNAStringSet-method Man page
sequenceQualityHist,SFFContainer-method Man page
sequenceQualityHist,ShortReadQ-method Man page
setVariantFilter Man page
setVariantFilter,AVASet-method Man page
setVariantFilter,MapperSet-method Man page
sff2fastq Man page
sff2fastq,SFFContainer-method Man page
variants Man page
writeSFF Man page Source code
R453Plus1Toolbox documentation built on Nov. 8, 2020, 5:59 p.m.

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