AVASet                  Creating an AVASet
AVASet-class            Class to contain Amplicon Variant Analyzer
                        Output
AnnotatedVariants-class
                        Class "AnnotatedVariants"
Breakpoints-class       Class "Breakpoints"
MapperSet               Creating a MapperSet
MapperSet-class         Class to Contain GS Reference Mapper Output
SFFContainer-class      Class '"SFFContainer"'
SFFRead-class           Class '"SFFRead"'
alignShortReads         Exact alignment of DNA sequences against a
                        reference
annotateVariants        Adds genomic information to variants
assayDataAmp            Access the amplicon data of an AVASet.
ava2vcf                 Convert an AVASet object into a VCF object
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
breakpointTable         Table of breakpoint support
breakpoints             Putative breakpoints of chimeric reads
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 reads
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 artificial chimeric reads.
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
mapperSetExample        GS Reference Mapper data import
mergeBreakpoints        Identify and merge related breakpoints caused
                        by the same variant.
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 region.
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
variants                Example data for 'plotVariants'
writeSFF                Function To Write Files In Roche's .sff Format
