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A B C D E F G H K L M N P Q R S V W misc
| addRead | Class '"SFFContainer"' |
| addRead-method | Class '"SFFContainer"' |
| alignedReadsC1 | Class "Breakpoints" |
| alignedReadsC1-method | Class "Breakpoints" |
| alignedReadsC1<- | Class "Breakpoints" |
| alignedReadsC1<--method | Class "Breakpoints" |
| alignedReadsC2 | Class "Breakpoints" |
| alignedReadsC2-method | Class "Breakpoints" |
| alignedReadsC2<- | Class "Breakpoints" |
| alignedReadsC2<--method | Class "Breakpoints" |
| alignShortReads | Exact alignment of DNA sequences against a reference |
| alignShortReads-method | Class to contain Amplicon Variant Analyzer Output |
| alignShortReads-method | Exact alignment of DNA sequences against a reference |
| annotatedVariants | Class "AnnotatedVariants" |
| AnnotatedVariants-class | Class "AnnotatedVariants" |
| annotatedVariants-method | Class "AnnotatedVariants" |
| annotatedVariants<--method | Class "AnnotatedVariants" |
| annotateVariants | Adds genomic information to variants |
| annotateVariants-method | Class to contain Amplicon Variant Analyzer Output |
| annotateVariants-method | Class to Contain GS Reference Mapper Output |
| annotateVariants-method | Adds genomic information to variants |
| assayDataAmp | Access the amplicon data of an AVASet. |
| assayDataAmp-method | Class to contain Amplicon Variant Analyzer Output |
| assayDataAmp<- | Class to contain Amplicon Variant Analyzer Output |
| assayDataAmp<--method | Class to contain Amplicon Variant Analyzer Output |
| ava2vcf | Convert an AVASet object into a VCF object |
| ava2vcf-method | Convert an AVASet object into a VCF object |
| AVASet | Creating an AVASet |
| AVASet-class | Class to contain Amplicon Variant Analyzer Output |
| AVASet-method | Creating an AVASet |
| 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. |
| baseFrequency-method | Absolute And Relative Frequency Of The Four Bases. |
| baseQualityHist | Plot A Histogram Of The Base Qualities. |
| baseQualityHist-method | Plot A Histogram Of The Base Qualities. |
| baseQualityStats | Statistics Of Base Quality |
| baseQualityStats-method | Statistics Of Base Quality |
| breakpoints | Putative breakpoints of chimeric reads |
| Breakpoints-class | Class "Breakpoints" |
| calculateTiTv | Calculate transition transversion ratio |
| calculateTiTv-method | Calculate transition transversion ratio |
| captureArray | Custom capture array design |
| clipAdapterLeft | Class '"SFFContainer"' |
| clipAdapterLeft-method | Class '"SFFContainer"' |
| clipAdapterLeft-method | Class '"SFFRead"' |
| clipAdapterLeft<- | Class '"SFFContainer"' |
| clipAdapterLeft<--method | Class '"SFFContainer"' |
| clipAdapterLeft<--method | Class '"SFFRead"' |
| clipAdapterRight | Class '"SFFContainer"' |
| clipAdapterRight-method | Class '"SFFContainer"' |
| clipAdapterRight-method | Class '"SFFRead"' |
| clipAdapterRight<- | Class '"SFFContainer"' |
| clipAdapterRight<--method | Class '"SFFContainer"' |
| clipAdapterRight<--method | Class '"SFFRead"' |
| clipQualityLeft | Class '"SFFContainer"' |
| clipQualityLeft-method | Class '"SFFContainer"' |
| clipQualityLeft-method | Class '"SFFRead"' |
| clipQualityLeft<- | Class '"SFFContainer"' |
| clipQualityLeft<--method | Class '"SFFContainer"' |
| clipQualityLeft<--method | Class '"SFFRead"' |
| clipQualityRight | Class '"SFFContainer"' |
| clipQualityRight-method | Class '"SFFContainer"' |
| clipQualityRight-method | Class '"SFFRead"' |
| clipQualityRight<- | Class '"SFFContainer"' |
| clipQualityRight<--method | Class '"SFFContainer"' |
| clipQualityRight<--method | Class '"SFFRead"' |
| commonAlignC1 | Class "Breakpoints" |
| commonAlignC1-method | Class "Breakpoints" |
| commonAlignC1<- | Class "Breakpoints" |
| commonAlignC1<--method | Class "Breakpoints" |
| commonAlignC2 | Class "Breakpoints" |
| commonAlignC2-method | Class "Breakpoints" |
| commonAlignC2<- | Class "Breakpoints" |
| commonAlignC2<--method | Class "Breakpoints" |
| commonBpsC1 | Class "Breakpoints" |
| commonBpsC1-method | Class "Breakpoints" |
| commonBpsC1<- | Class "Breakpoints" |
| commonBpsC1<--method | Class "Breakpoints" |
| commonBpsC2 | Class "Breakpoints" |
| commonBpsC2-method | Class "Breakpoints" |
| commonBpsC2<- | Class "Breakpoints" |
| commonBpsC2<--method | Class "Breakpoints" |
| complexity.dust | Sequence Complexity Using The DUST Algorithm |
| complexity.dust-method | Sequence Complexity Using The DUST Algorithm |
| complexity.entropy | Sequence Complexity Using The Shannon-Wiener Algorithm |
| complexity.entropy-method | Sequence Complexity Using The Shannon-Wiener Algorithm |
| convertCigar | Basic functions for CIGAR strings |
| coverageOnTarget | Computes the coverage restricted to the target region. |
| coverageOnTarget-method | Computes the coverage restricted to the target region. |
| demultiplexReads | Performs MID/Multiplex filtering |
| demultiplexReads-method | Performs MID/Multiplex filtering |
| detectBreakpoints | Clustering and consensus breakpoint detection for chimeric reads |
| detectBreakpoints-method | Clustering and consensus breakpoint detection for chimeric reads |
| dinucleotideOddsRatio | Dinucleotide Odds Ratio |
| dinucleotideOddsRatio-method | Dinucleotide Odds Ratio |
| extendedCIGARToList | Basic functions for CIGAR strings |
| fDataAmp | Access the amplicon data of an AVASet. |
| fDataAmp-method | Class to contain Amplicon Variant Analyzer Output |
| featureDataAmp | Access the amplicon data of an AVASet |
| featureDataAmp-method | Class to contain Amplicon Variant Analyzer Output |
| featureDataAmp<- | Class to contain Amplicon Variant Analyzer Output |
| featureDataAmp<--method | Class to contain Amplicon Variant Analyzer Output |
| filterChimericReads | Extract chimeric reads and apply filtering steps to remove artificial chimeric reads. |
| filterChimericReads-method | Extract chimeric reads and apply filtering steps to remove artificial chimeric reads. |
| flowChars | Class '"SFFContainer"' |
| flowChars-method | Class '"SFFContainer"' |
| flowChars-method | Class '"SFFRead"' |
| flowChars<- | Class '"SFFContainer"' |
| flowChars<--method | Class '"SFFContainer"' |
| flowChars<--method | Class '"SFFRead"' |
| flowgram | Class '"SFFRead"' |
| flowgram-method | Class '"SFFRead"' |
| flowgram<- | Class '"SFFRead"' |
| flowgram<--method | Class '"SFFRead"' |
| flowgramBarplot | Create A Barplot Of The Flow Intensities |
| flowgramBarplot-method | Create A Barplot Of The Flow Intensities |
| flowgramFormat | Class '"SFFContainer"' |
| flowgramFormat-method | Class '"SFFContainer"' |
| flowgramFormat-method | Class '"SFFRead"' |
| flowgramFormat<- | Class '"SFFContainer"' |
| flowgramFormat<--method | Class '"SFFContainer"' |
| flowgramFormat<--method | Class '"SFFRead"' |
| flowgrams | Class '"SFFContainer"' |
| flowgrams-method | Class '"SFFContainer"' |
| flowgrams<- | Class '"SFFContainer"' |
| flowgrams<--method | Class '"SFFContainer"' |
| flowIndexes | Class '"SFFContainer"' |
| flowIndexes-method | Class '"SFFContainer"' |
| flowIndexes-method | Class '"SFFRead"' |
| flowIndexes<- | Class '"SFFContainer"' |
| flowIndexes<--method | Class '"SFFContainer"' |
| flowIndexes<--method | Class '"SFFRead"' |
| gcContent | Calculate The Overall GC-Content |
| gcContent-method | Calculate The Overall GC-Content |
| gcContentHist | GC-Content Histogram |
| gcContentHist-method | GC-Content Histogram |
| gcPerPosition | GC-Content Per Position |
| gcPerPosition-method | GC-Content Per Position |
| genomeSequencerMIDs | Retrieve GS multiplex sequences |
| genomeSequencerMIDs-method | Retrieve GS multiplex sequences |
| getAlignedReads | Import reads from an Amplicon Variant Analyzer project |
| getAlignedReads-method | Import reads from an Amplicon Variant Analyzer project |
| getAminoAbbr | Get amino acid abbreviations |
| getRead | Class '"SFFContainer"' |
| getRead-method | Class '"SFFContainer"' |
| getReadStatus | Class to Contain GS Reference Mapper Output |
| getReadStatus-method | Class to Contain GS Reference Mapper Output |
| getVariantPercentages | Variant coverage |
| getVariantPercentages-method | Class to contain Amplicon Variant Analyzer Output |
| getVariantPercentages-method | Class to Contain GS Reference Mapper Output |
| homopolymerHist | Create A Histogram Of The Homopolymer Stretches |
| homopolymerHist-method | Create A Histogram Of The Homopolymer Stretches |
| htmlReport | HTML-Report Builder for the AVASet and MapperSet |
| htmlReport-method | Class to contain Amplicon Variant Analyzer Output |
| htmlReport-method | Class to Contain GS Reference Mapper Output |
| keySequence | Class '"SFFContainer"' |
| keySequence-method | Class '"SFFContainer"' |
| keySequence-method | Class '"SFFRead"' |
| keySequence<- | Class '"SFFContainer"' |
| keySequence<--method | Class '"SFFContainer"' |
| keySequence<--method | Class '"SFFRead"' |
| length-method | Class "Breakpoints" |
| listToExtendedCIGAR | Basic functions for CIGAR strings |
| MapperSet | Creating a MapperSet |
| MapperSet-class | Class to Contain GS Reference Mapper Output |
| MapperSet-method | Creating a MapperSet |
| mapperSetExample | GS Reference Mapper data import |
| mergeBreakpoints | Identify and merge related breakpoints caused by the same variant. |
| mergeBreakpoints-method | Class "Breakpoints" |
| mutationInfo | Example data for 'plotVariants' |
| name | Class '"SFFContainer"' |
| name-method | Class '"SFFContainer"' |
| name-method | Class '"SFFRead"' |
| name<- | Class '"SFFContainer"' |
| name<--method | Class '"SFFContainer"' |
| name<--method | Class '"SFFRead"' |
| names-method | Class "AnnotatedVariants" |
| names-method | Class "Breakpoints" |
| names<--method | Class "AnnotatedVariants" |
| names<--method | Class "Breakpoints" |
| nucleotideCharts | Nucleotide Charts |
| nucleotideCharts-method | Nucleotide Charts |
| plotAmpliconCoverage | Creates a plot visualizing the number of reads per amplicon |
| plotAmpliconCoverage-method | Creates a plot visualizing the number of reads per amplicon |
| plotChimericReads | Plots chimeric reads |
| plotChimericReads-method | Class "Breakpoints" |
| plotVariants | Plots variant positions |
| plotVariants-method | Plots variant positions |
| plotVariationFrequency | Create an AVA style variation frequency plot |
| plotVariationFrequency-method | Create an AVA style variation frequency plot |
| positionQualityBoxplot | Boxplot Of The Quality For Each Position |
| positionQualityBoxplot-method | Boxplot Of The Quality For Each Position |
| quality-method | Class '"SFFRead"' |
| quality<- | Class '"SFFRead"' |
| quality<--method | Class '"SFFRead"' |
| qualityReportSFF | Function To Create A Quality Report In PDF Format |
| read | Class '"SFFRead"' |
| read-method | Class '"SFFRead"' |
| read<- | Class '"SFFRead"' |
| read<--method | Class '"SFFRead"' |
| readLengthHist | Histogram Of The Read Lengths |
| readLengthHist-method | Histogram Of The Read Lengths |
| readLengthStats | Statistics For The Read Lengths |
| readLengthStats-method | Statistics For The Read Lengths |
| reads | Class '"SFFContainer"' |
| reads-method | Class '"SFFContainer"' |
| reads<- | Class '"SFFContainer"' |
| reads<--method | Class '"SFFContainer"' |
| readSFF | Function To Read In Roche's .sff Files |
| readsOnTarget | Check for each read whether it aligns within the given region. |
| readsOnTarget-method | Check for each read whether it aligns within the given region. |
| referenceSequences | Access the reference sequences of an AVASet |
| referenceSequences-method | Class to contain Amplicon Variant Analyzer Output |
| referenceSequences<- | Class to contain Amplicon Variant Analyzer Output |
| referenceSequences<--method | Class to contain Amplicon Variant Analyzer Output |
| regions | Example data for 'plotVariants' |
| removeLinker | Remove linker sequences located at the start of short reads |
| removeLinker-method | Remove linker sequences located at the start of short reads |
| seqsC1 | Class "Breakpoints" |
| seqsC1-method | Class "Breakpoints" |
| seqsC1<- | Class "Breakpoints" |
| seqsC1<--method | Class "Breakpoints" |
| seqsC2 | Class "Breakpoints" |
| seqsC2-method | Class "Breakpoints" |
| seqsC2<- | Class "Breakpoints" |
| seqsC2<--method | Class "Breakpoints" |
| sequenceCaptureLinkers | Retrieve NimbleGen's sequence capture linkers |
| sequenceCaptureLinkers-method | Retrieve NimbleGen's sequence capture linkers |
| sequenceQualityHist | A Histogram Of The Sequence Qualities |
| sequenceQualityHist-method | A Histogram Of The Sequence Qualities |
| setVariantFilter | Filters output of variant information |
| setVariantFilter-method | Class to contain Amplicon Variant Analyzer Output |
| setVariantFilter-method | Class to Contain GS Reference Mapper Output |
| sff2fastq | Write A SFFContainer Object To A FASTQ File |
| sff2fastq-method | Write A SFFContainer Object To A FASTQ File |
| SFFContainer | Class '"SFFContainer"' |
| SFFContainer-class | Class '"SFFContainer"' |
| SFFRead | Class '"SFFRead"' |
| SFFRead-class | Class '"SFFRead"' |
| variants | Example data for 'plotVariants' |
| writeSFF | Function To Write Files In Roche's .sff Format |
| [-method | Class to contain Amplicon Variant Analyzer Output |
| [-method | Class "Breakpoints" |
| [-method | Class '"SFFContainer"' |