A B C D E F G H K L M N P Q R S V 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 |
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"' |
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' |
[-method | Class to contain Amplicon Variant Analyzer Output |
[-method | Class "Breakpoints" |
[-method | Class '"SFFContainer"' |