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
alignShortReads         Exact alignment of DNA sequences against a
                        reference
annotateVariants        Adds genomic information to variants
assayDataAmp            Access the amplicon data of 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
calculateTiTv           Calculate transition transversion ratio
captureArray            Custom capture array design
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
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.
genomeSequencerMIDs     Retrieve GS multiplex sequences
getAlignedReads         Import reads from an Amplicon Variant Analyzer
                        project
getAminoAbbr            Get amino acid abbreviations
getVariantPercentages   Variant coverage
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.
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
readsOnTarget           Check for each read whether it aligns within
                        the given region.
referenceSequences      Access the reference sequences of an AVASet
removeLinker            Remove linker sequences located at the start of
                        short reads
sequenceCaptureLinkers
                        Retrieve NimbleGen's sequence capture linkers
setVariantFilter        Filters output of variant information
transcriptdf            Ensembl transcript information for variant
                        plotting
