A B C D E F G H L M N P R S T misc
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 |
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 |
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" |
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 |
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. |
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 |
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 |
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 |
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" |
names-method | Class "AnnotatedVariants" |
names-method | Class "Breakpoints" |
names<--method | Class "AnnotatedVariants" |
names<--method | Class "Breakpoints" |
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 |
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 |
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 |
setVariantFilter | Filters output of variant information |
setVariantFilter-method | Class to contain Amplicon Variant Analyzer Output |
setVariantFilter-method | Class to Contain GS Reference Mapper Output |
transcriptdf | Ensembl transcript information for variant plotting |
[-method | Class to contain Amplicon Variant Analyzer Output |
[-method | Class "Breakpoints" |