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

Global functions
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
addComma Source code
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
alignShortReads_AVASet Source code
alignShortReads_DNAStringSet Source code
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
annotateReference Source code
annotateVariantBlock Source code
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
annotateVariants_AVASet Source code
annotateVariants_MapperSet Source code
annotateVariants_data.frame Source code
annotatedVariants Man page
annotatedVariants,AnnotatedVariants-method Man page
annotatedVariants<-,AnnotatedVariants,list-method Man page
annotatedVariants_to_dataFrame Source code
assayDataAmp Man page
assayDataAmp,AVASet-method Man page
assayDataAmp<- Man page
assayDataAmp<-,AVASet,AssayData-method Man page
ava2vcf Man page Source code
ava2vcf,AVASet-method Man page
avaSetExample Man page
avaSetFiltered Man page
avaSetFiltered_annot Man page
baseFrequency Man page Source code
baseFrequency,DNAStringSet-method Man page
baseFrequency,SFFContainer-method Man page
baseFrequency,ShortRead-method Man page
baseFrequency_sff Source code
baseFrequency_sr Source code
baseQualityHist Man page Source code
baseQualityHist,QualityScaledDNAStringSet-method Man page
baseQualityHist,SFFContainer-method Man page
baseQualityHist,ShortReadQ-method Man page
baseQualityHist_sff Source code
baseQualityHist_sr Source code
baseQualityStats Man page Source code
baseQualityStats,QualityScaledDNAStringSet-method Man page
baseQualityStats,SFFContainer-method Man page
baseQualityStats,ShortReadQ-method Man page
baseQualityStats_sff Source code
baseQualityStats_sr Source code
breakpoints Man page
calculateTiTv Man page Source code
calculateTiTv,AVASet-method Man page
calculateTiTv,MapperSet-method Man page
captureArray Man page
catchBadInput Source code
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
codingRegion Source code
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
complementStrand Source code
complexity.dust Man page Source code
complexity.dust,DNAStringSet-method Man page
complexity.dust,SFFContainer-method Man page
complexity.dust,ShortRead-method Man page
complexity.dust_sff Source code
complexity.dust_sr Source code
complexity.entropy Man page Source code
complexity.entropy,DNAStringSet-method Man page
complexity.entropy,SFFContainer-method Man page
complexity.entropy,ShortRead-method Man page
complexity.entropy_sff Source code
complexity.entropy_sr Source code
computeBPDistance_nsc Source code
computeBPDistance_sc Source code
computeLocalCoordinates Source code
convertCigar Man page
coverageOnTarget Man page Source code
coverageOnTarget,list,RangesList-method Man page
createNavigation Source code
demultiplexReads Man page Source code
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 Source code
detectBreakpoints,list-method Man page
dinucleotideOddsRatio Man page Source code
dinucleotideOddsRatio,DNAStringSet-method Man page
dinucleotideOddsRatio,SFFContainer-method Man page
dinucleotideOddsRatio,ShortRead-method Man page
dinucleotideOddsRatio_sff Source code
dinucleotideOddsRatio_sr Source code
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 Source code
filterChimericReads,list,RangesList,DNAString,missing,missing-me Man page
filterChimericReads,list,RangesList,DNAString,numeric,numeric-me Man page
filterChimericReads,list,RangesList,missing,missing,missing-meth Man page
filterChimericReads,list,RangesList,missing,numeric,numeric-meth 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 Source code
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 Source code
gcContent,DNAStringSet-method Man page
gcContent,SFFContainer-method Man page
gcContent,ShortRead-method Man page
gcContentHist Man page Source code
gcContentHist,DNAStringSet-method Man page
gcContentHist,SFFContainer-method Man page
gcContentHist,ShortRead-method Man page
gcContentHist_sff Source code
gcContentHist_sr Source code
gcContent_sff Source code
gcContent_sr Source code
gcPerPosition Man page Source code
gcPerPosition,DNAStringSet-method Man page
gcPerPosition,SFFContainer-method Man page
gcPerPosition,ShortRead-method Man page
gcPerPosition_sff Source code
gcPerPosition_sr Source code
genomeSequencerMIDs Man page Source code
genomeSequencerMIDs,character-method Man page
genomeSequencerMIDs,missing-method Man page
genomeSequencerMIDs_character Source code
getAlignedReads Man page Source code
getAlignedReads,AVASet-method Man page
getAminoAbbr Man page Source code
getEnsemblInfo Source code
getMutations Source code
getRead Man page
getRead,SFFContainer,character-method Man page
getReadStatus Man page
getReadStatus,MapperSet-method Man page
getVariantPercentages Man page Source code
getVariantPercentages,AVASet-method Man page
getVariantPercentages,MapperSet-method Man page
homopolymerHist Man page Source code
homopolymerHist,SFFRead-method Man page
htmlReport Man page Source code
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
markRelatedBreakpoints Source code
mergeBreakpoints Man page Source code
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
nitHtmlReportAVASet Source code
nitHtmlReportGSMSet Source code
nitializePlot Source code
nucleotideCharts Man page Source code
nucleotideCharts,DNAStringSet-method Man page
nucleotideCharts,SFFContainer-method Man page
nucleotideCharts,ShortRead-method Man page
nucleotideCharts_sff Source code
nucleotideCharts_sr Source code
plotAmpliconCoverage Man page Source code
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 Source code
plotChimericReads,Breakpoints-method Man page
plotMutations Source code
plotMutationsBasePairPlot Source code
plotReads Source code
plotReadsBasePairs Source code
plotReference Source code
plotReferenceBasePairs Source code
plotVariants Man page Source code
plotVariants,AnnotatedVariants,character-method Man page
plotVariants,data.frame,character-method Man page
plotVariationFrequency Man page
plotVariationFrequency,character,numeric-method Man page
plotVariationFrequency_data.frame Source code
plotVariationFrequency_file Source code
positionQualityBoxplot Man page Source code
positionQualityBoxplot,QualityScaledDNAStringSet-method Man page
positionQualityBoxplot,SFFContainer-method Man page
positionQualityBoxplot,ShortReadQ-method Man page
positionQualityBoxplot_sff Source code
positionQualityBoxplot_sr Source code
quality,SFFRead-method Man page
quality<- Man page
quality<-,SFFRead,BString-method Man page
qualityReport Source code
qualityReportSFF Man page Source code
read Man page
read,SFFRead-method Man page
read454BaseCallerMetrics_character Source code
read454QualityFilterMetrics_character Source code
read<- Man page
read<-,SFFRead,QualityScaledDNAStringSet-method Man page
readGSMAssayFeatureData Source code
readGSMPhenoData Source code
readLengthHist Man page Source code
readLengthHist,DNAStringSet-method Man page
readLengthHist,SFFContainer-method Man page
readLengthHist,ShortRead-method Man page
readLengthHist_sff Source code
readLengthHist_sr Source code
readLengthStats Man page Source code
readLengthStats,DNAStringSet-method Man page
readLengthStats,SFFContainer-method Man page
readLengthStats,ShortRead-method Man page
readLengthStats_sff Source code
readLengthStats_sr Source code
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 Source code
readsOnTarget,list,RangesList-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 Source code
removeLinker,XStringSet,DNAString,logical,numeric,numeric-method Man page
removeLinker,XStringSet,DNAString,missing,missing,missing-method Man page
removeSoftclips Source code
reverseC2 Source code
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 Source code
sequenceCaptureLinkers,character-method Man page
sequenceCaptureLinkers,missing-method Man page
sequenceCaptureLinkers_character Source code
sequenceQualityHist Man page Source code
sequenceQualityHist,QualityScaledDNAStringSet-method Man page
sequenceQualityHist,SFFContainer-method Man page
sequenceQualityHist,ShortReadQ-method Man page
sequenceQualityHist_sff Source code
sequenceQualityHist_sr Source code
setVariantFilter Man page Source code
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
Bioconductor-mirror/R453Plus1Toolbox documentation built on May 31, 2017, 10:39 p.m.