R453Plus1Toolbox: A package for importing and analyzing data from Roche's Genome Sequencer System
Version 1.26.0

The R453Plus1 Toolbox comprises useful functions for the analysis of data generated by Roche's 454 sequencing platform. It adds functions for quality assurance as well as for annotation and visualization of detected variants, complementing the software tools shipped by Roche with their product. Further, a pipeline for the detection of structural variants is provided.

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AuthorHans-Ulrich Klein, Christoph Bartenhagen, Christian Ruckert
Bioconductor views DataImport DataRepresentation Infrastructure QualityControl ReportWriting Sequencing Visualization
Date of publicationNone
MaintainerHans-Ulrich Klein <h.klein@uni-muenster.de>
LicenseLGPL-3
Version1.26.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("R453Plus1Toolbox")

Man pages

alignShortReads: Exact alignment of DNA sequences against a reference
AnnotatedVariants-class: Class "AnnotatedVariants"
annotateVariants: Adds genomic information to variants
assayDataAmp: Access the amplicon data of an AVASet.
ava2vcf: Convert an AVASet object into a VCF object
AVASet: Creating an AVASet
AVASet-class: Class to contain Amplicon Variant Analyzer Output
avaSetExample: Amplicon Variant Analyzer data import
avaSetFiltered: Amplicon Variant Analyzer data import
avaSetFiltered_annot: AVASet variant annotations
baseFrequency: Absolute And Relative Frequency Of The Four Bases.
baseQualityHist: Plot A Histogram Of The Base Qualities.
baseQualityStats: Statistics Of Base Quality
breakpoints: Putative breakpoints of chimeric reads
Breakpoints-class: Class "Breakpoints"
calculateTiTv: Calculate transition transversion ratio
captureArray: Custom capture array design
complexity.dust: Sequence Complexity Using The DUST Algorithm
complexity.entropy: Sequence Complexity Using The Shannon-Wiener Algorithm
convertCigar: Basic functions for CIGAR strings
coverageOnTarget: Computes the coverage restricted to the target region.
demultiplexReads: Performs MID/Multiplex filtering
detectBreakpoints: Clustering and consensus breakpoint detection for chimeric...
dinucleotideOddsRatio: Dinucleotide Odds Ratio
fDataAmp: Access the amplicon data of an AVASet.
featureDataAmp: Access the amplicon data of an AVASet
filterChimericReads: Extract chimeric reads and apply filtering steps to remove...
flowgramBarplot: Create A Barplot Of The Flow Intensities
gcContent: Calculate The Overall GC-Content
gcContentHist: GC-Content Histogram
gcPerPosition: GC-Content Per Position
genomeSequencerMIDs: Retrieve GS multiplex sequences
getAlignedReads: Import reads from an Amplicon Variant Analyzer project
getAminoAbbr: Get amino acid abbreviations
getVariantPercentages: Variant coverage
homopolymerHist: Create A Histogram Of The Homopolymer Stretches
htmlReport: HTML-Report Builder for the AVASet and MapperSet
MapperSet: Creating a MapperSet
MapperSet-class: Class to Contain GS Reference Mapper Output
mapperSetExample: GS Reference Mapper data import
mergeBreakpoints: Identify and merge related breakpoints caused by the same...
mutationInfo: Example data for 'plotVariants'
nucleotideCharts: Nucleotide Charts
plotAmpliconCoverage: Creates a plot visualizing the number of reads per amplicon
plotChimericReads: Plots chimeric reads
plotVariants: Plots variant positions
plotVariationFrequency: Create an AVA style variation frequency plot
positionQualityBoxplot: Boxplot Of The Quality For Each Position
qualityReportSFF: Function To Create A Quality Report In PDF Format
readLengthHist: Histogram Of The Read Lengths
readLengthStats: Statistics For The Read Lengths
readSFF: Function To Read In Roche's .sff Files
readsOnTarget: Check for each read whether it aligns within the given...
referenceSequences: Access the reference sequences of an AVASet
regions: Example data for 'plotVariants'
removeLinker: Remove linker sequences located at the start of short reads
sequenceCaptureLinkers: Retrieve NimbleGen's sequence capture linkers
sequenceQualityHist: A Histogram Of The Sequence Qualities
setVariantFilter: Filters output of variant information
sff2fastq: Write A SFFContainer Object To A FASTQ File
SFFContainer-class: Class '"SFFContainer"'
SFFRead-class: Class '"SFFRead"'
variants: Example data for 'plotVariants'
writeSFF: Function To Write Files In Roche's .sff Format

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

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/AllGenerics.R
R/alignShortReads.R
R/annotateVariants.R
R/ava2vcf.R
R/calculateTiTv.R
R/convertCigar.R
R/coverageOnTarget.R
R/demultiplexReads.R
R/detectBreakpoints.R
R/filterChimericReads.R
R/filterVariants.R
R/genomeSequencerMIDs.R
R/getAlignedReads.R
R/getAminoAbbr.R
R/htmlReport.R
R/mergeBreakpoints.R
R/methods-AVASet.R
R/methods-AnnotatedVariants.R
R/methods-Breakpoints.R
R/methods-MapperSet.R
R/methods-Roche454BaseCallerMetrics.R
R/methods-Roche454QualityFilterMetrics.R
R/methods-SFFContainer.R
R/methods-SFFRead.R
R/plotAmpliconCoverage.R
R/plotChimericReads.R
R/plotVariants.R
R/plotVariationFrequency.R
R/qualityControl.R
R/qualityReportSFF.R
R/read454BaseCallerMetrics.R
R/read454QualityFilterMetrics.R
R/readSFF.R
R/readsOnTarget.R
R/removeLinker.R
R/sequenceCaptureLinkers.R
R/writeSFF.R
build
build/vignette.rds
data
data/avaSetExample.RData
data/avaSetFiltered.RData
data/avaSetFiltered_annot.RData
data/breakpoints.RData
data/captureArray.RData
data/mapperSetExample.RData
data/plotVariantsExample.RData
inst
inst/CITATION
inst/NEWS.Rd
inst/doc
inst/doc/vignette.R
inst/doc/vignette.Rnw
inst/doc/vignette.pdf
inst/extdata
inst/extdata/AVASet
inst/extdata/AVASet/Amplicons
inst/extdata/AVASet/Amplicons/ProjectDef
inst/extdata/AVASet/Amplicons/ProjectDef/ampliconsProject.txt
inst/extdata/AVASet/Amplicons/Results
inst/extdata/AVASet/Amplicons/Results/Align
inst/extdata/AVASet/Amplicons/Results/Align/I116
inst/extdata/AVASet/Amplicons/Results/Align/I116/I36
inst/extdata/AVASet/Amplicons/Results/Align/I116/I36/I116_vs_I36.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Align/I116/I37
inst/extdata/AVASet/Amplicons/Results/Align/I116/I37/I116_vs_I37.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Align/I116/I40
inst/extdata/AVASet/Amplicons/Results/Align/I116/I40/I116_vs_I40.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Align/I116/I42
inst/extdata/AVASet/Amplicons/Results/Align/I116/I42/I116_vs_I42.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Align/I117
inst/extdata/AVASet/Amplicons/Results/Align/I117/I36
inst/extdata/AVASet/Amplicons/Results/Align/I117/I36/I117_vs_I36.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Align/I117/I37
inst/extdata/AVASet/Amplicons/Results/Align/I117/I37/I117_vs_I37.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Align/I117/I40
inst/extdata/AVASet/Amplicons/Results/Align/I117/I40/I117_vs_I40.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Align/I117/I42
inst/extdata/AVASet/Amplicons/Results/Align/I117/I42/I117_vs_I42.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Align/I118
inst/extdata/AVASet/Amplicons/Results/Align/I118/I36
inst/extdata/AVASet/Amplicons/Results/Align/I118/I36/I118_vs_I36.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Align/I118/I37
inst/extdata/AVASet/Amplicons/Results/Align/I118/I37/I118_vs_I37.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Align/I118/I40
inst/extdata/AVASet/Amplicons/Results/Align/I118/I40/I118_vs_I40.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Align/I118/I42
inst/extdata/AVASet/Amplicons/Results/Align/I118/I42/I118_vs_I42.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Align/I9644
inst/extdata/AVASet/Amplicons/Results/Align/I9644/I36
inst/extdata/AVASet/Amplicons/Results/Align/I9644/I36/I9644_vs_I36.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Align/I9644/I37
inst/extdata/AVASet/Amplicons/Results/Align/I9644/I37/I9644_vs_I37.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Align/I9644/I40
inst/extdata/AVASet/Amplicons/Results/Align/I9644/I40/I9644_vs_I40.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Align/I9644/I42
inst/extdata/AVASet/Amplicons/Results/Align/I9644/I42/I9644_vs_I42.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Align/I9645
inst/extdata/AVASet/Amplicons/Results/Align/I9645/I36
inst/extdata/AVASet/Amplicons/Results/Align/I9645/I36/I9645_vs_I36.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Align/I9645/I37
inst/extdata/AVASet/Amplicons/Results/Align/I9645/I37/I9645_vs_I37.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Align/I9645/I40
inst/extdata/AVASet/Amplicons/Results/Align/I9645/I40/I9645_vs_I40.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Align/I9645/I42
inst/extdata/AVASet/Amplicons/Results/Align/I9645/I42/I9645_vs_I42.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Align/I9646
inst/extdata/AVASet/Amplicons/Results/Align/I9646/I36
inst/extdata/AVASet/Amplicons/Results/Align/I9646/I36/I9646_vs_I36.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Align/I9646/I37
inst/extdata/AVASet/Amplicons/Results/Align/I9646/I37/I9646_vs_I37.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Align/I9646/I37/I9646_vs_I37.readAlign.txt
inst/extdata/AVASet/Amplicons/Results/Align/I9646/I40
inst/extdata/AVASet/Amplicons/Results/Align/I9646/I40/I9646_vs_I40.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Align/I9646/I42
inst/extdata/AVASet/Amplicons/Results/Align/I9646/I42/I9646_vs_I42.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Variants
inst/extdata/AVASet/Amplicons/Results/Variants/I116
inst/extdata/AVASet/Amplicons/Results/Variants/I116/I116xI36detectedVariants.txt
inst/extdata/AVASet/Amplicons/Results/Variants/I116/I116xI37detectedVariants.txt
inst/extdata/AVASet/Amplicons/Results/Variants/I116/I116xI40detectedVariants.txt
inst/extdata/AVASet/Amplicons/Results/Variants/I116/I116xI42detectedVariants.txt
inst/extdata/AVASet/Amplicons/Results/Variants/I117
inst/extdata/AVASet/Amplicons/Results/Variants/I117/I117xI36detectedVariants.txt
inst/extdata/AVASet/Amplicons/Results/Variants/I117/I117xI37detectedVariants.txt
inst/extdata/AVASet/Amplicons/Results/Variants/I117/I117xI40detectedVariants.txt
inst/extdata/AVASet/Amplicons/Results/Variants/I117/I117xI42detectedVariants.txt
inst/extdata/AVASet/Amplicons/Results/Variants/I118
inst/extdata/AVASet/Amplicons/Results/Variants/I118/I118xI36detectedVariants.txt
inst/extdata/AVASet/Amplicons/Results/Variants/I118/I118xI37detectedVariants.txt
inst/extdata/AVASet/Amplicons/Results/Variants/I118/I118xI40detectedVariants.txt
inst/extdata/AVASet/Amplicons/Results/Variants/I118/I118xI42detectedVariants.txt
inst/extdata/AVASet/Amplicons/Results/Variants/I9644
inst/extdata/AVASet/Amplicons/Results/Variants/I9644/I9644xI36detectedVariants.txt
inst/extdata/AVASet/Amplicons/Results/Variants/I9644/I9644xI37detectedVariants.txt
inst/extdata/AVASet/Amplicons/Results/Variants/I9644/I9644xI40detectedVariants.txt
inst/extdata/AVASet/Amplicons/Results/Variants/I9644/I9644xI42detectedVariants.txt
inst/extdata/AVASet/Amplicons/Results/Variants/I9645
inst/extdata/AVASet/Amplicons/Results/Variants/I9645/I9645xI36detectedVariants.txt
inst/extdata/AVASet/Amplicons/Results/Variants/I9645/I9645xI37detectedVariants.txt
inst/extdata/AVASet/Amplicons/Results/Variants/I9645/I9645xI40detectedVariants.txt
inst/extdata/AVASet/Amplicons/Results/Variants/I9645/I9645xI42detectedVariants.txt
inst/extdata/AVASet/Amplicons/Results/Variants/I9646
inst/extdata/AVASet/Amplicons/Results/Variants/I9646/I9646xI36detectedVariants.txt
inst/extdata/AVASet/Amplicons/Results/Variants/I9646/I9646xI37detectedVariants.txt
inst/extdata/AVASet/Amplicons/Results/Variants/I9646/I9646xI40detectedVariants.txt
inst/extdata/AVASet/Amplicons/Results/Variants/I9646/I9646xI42detectedVariants.txt
inst/extdata/AVASet/Amplicons/Results/Variants/currentVariantDefs.txt
inst/extdata/AVASet_doAmplicon
inst/extdata/AVASet_doAmplicon/amp.csv
inst/extdata/AVASet_doAmplicon/reference.csv
inst/extdata/AVASet_doAmplicon/sample.csv
inst/extdata/AVASet_doAmplicon/variant.csv
inst/extdata/AVASet_doAmplicon/variantHits.csv
inst/extdata/AVAVarFreqExport
inst/extdata/AVAVarFreqExport/AVAVarFreqExport.xls
inst/extdata/MapperSet
inst/extdata/MapperSet/N01
inst/extdata/MapperSet/N01/mapping
inst/extdata/MapperSet/N01/mapping/454HCDiffs.txt
inst/extdata/MapperSet/N01/mapping/454NewblerMetrics.txt
inst/extdata/MapperSet/N03
inst/extdata/MapperSet/N03/mapping
inst/extdata/MapperSet/N03/mapping/454HCDiffs.txt
inst/extdata/MapperSet/N03/mapping/454NewblerMetrics.txt
inst/extdata/MapperSet/N04
inst/extdata/MapperSet/N04/mapping
inst/extdata/MapperSet/N04/mapping/454HCDiffs.txt
inst/extdata/MapperSet/N04/mapping/454NewblerMetrics.txt
inst/extdata/SFF
inst/extdata/SFF/example.sff
inst/extdata/SVDetection
inst/extdata/SVDetection/R_2009_07_30
inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31
inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/1.CAT.454Reads.fna
inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/1.CAT.454Reads.qual
inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/1.TCA.454Reads.fna
inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/1.TCA.454Reads.qual
inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/2.CAT.454Reads.fna
inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/2.CAT.454Reads.qual
inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/2.TCA.454Reads.fna
inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/2.TCA.454Reads.qual
inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/454BaseCallerMetrics.csv
inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/454BaseCallerMetrics.txt
inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/454DataProcessingDir.xml
inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/454QualityFilterMetrics.csv
inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/454QualityFilterMetrics.txt
inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/454RuntimeMetricsAll.csv
inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/454RuntimeMetricsAll.txt
inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/dataRunParams.xml
inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/gsRunProcessor.log
inst/extdata/SVDetection/bam
inst/extdata/SVDetection/bam/N01.bam
inst/extdata/SVDetection/chip
inst/extdata/SVDetection/chip/CaptureArray_hg19.bed
inst/extdata/qualityReport.Rnw
inst/javascript
inst/javascript/sorttable.js
man
man/AVASet-class.Rd
man/AVASet.Rd
man/AnnotatedVariants-class.Rd
man/Breakpoints-class.Rd
man/MapperSet-class.Rd
man/MapperSet.Rd
man/SFFContainer-class.Rd
man/SFFRead-class.Rd
man/alignShortReads.Rd
man/annotateVariants.Rd
man/assayDataAmp.Rd
man/ava2vcf.Rd
man/avaSetExample.Rd
man/avaSetFiltered.Rd
man/avaSetFiltered_annot.Rd
man/baseFrequency.Rd
man/baseQualityHist.Rd
man/baseQualityStats.Rd
man/breakpoints.Rd
man/calculateTiTv.Rd
man/captureArray.Rd
man/complexity.dust.Rd
man/complexity.entropy.Rd
man/convertCigar.Rd
man/coverageOnTarget.Rd
man/demultiplexReads.Rd
man/detectBreakpoints.Rd
man/dinucleotideOddsRatio.Rd
man/fDataAmp.Rd
man/featureDataAmp.Rd
man/filterChimericReads.Rd
man/flowgramBarplot.Rd
man/gcContent.Rd
man/gcContentHist.Rd
man/gcPerPosition.Rd
man/genomeSequencerMIDs.Rd
man/getAlignedReads.Rd
man/getAminoAbbr.Rd
man/getVariantPercentages.Rd
man/homopolymerHist.Rd
man/htmlReport.Rd
man/mapperSetExample.Rd
man/mergeBreakpoints.Rd
man/mutationInfo.Rd
man/nucleotideCharts.Rd
man/plotAmpliconCoverage.Rd
man/plotChimericReads.Rd
man/plotVariants.Rd
man/plotVariationFrequency.Rd
man/positionQualityBoxplot.Rd
man/qualityReportSFF.Rd
man/readLengthHist.Rd
man/readLengthStats.Rd
man/readSFF.Rd
man/readsOnTarget.Rd
man/referenceSequences.Rd
man/regions.Rd
man/removeLinker.Rd
man/sequenceCaptureLinkers.Rd
man/sequenceQualityHist.Rd
man/setVariantFilter.Rd
man/sff2fastq.Rd
man/variants.Rd
man/writeSFF.Rd
src
src/io_lib
src/io_lib/os.h
src/readSFF.c
src/readSFF.h
src/writeSFF.c
src/writeSFF.h
vignettes
vignettes/vignette.Rnw
R453Plus1Toolbox documentation built on May 20, 2017, 9:53 p.m.