.checkReferenceAnchor   Checks if mutations and reference genome
                        correspond
checkProteotypicFragments
                        Determine proteotypic fragments within the
                        translated CDS
exportProteoDiscography
                        Export the generated (mutant) peptides
                        sequences to a FASTA database.
generateJunctionModels
                        Generate putative transcript-models derived
                        from splice-junctions.
generateProteoDiscography
                        Generate the annotation database
                        (ProteoDiscography)
getDiscography          Retrieve imported genomic variants,
                        splice-junctions and manual sequences.
importGenomicVariants   Import genomic variants into the
                        ProteoDiscography
importGenomicVariants.MAF
                        Import MAF files into a ProteoDiscography.
importGenomicVariants.VCF
                        Import VCF files into a ProteoDiscography.
importSpliceJunctions   Import splice-junctions into the
                        ProteoDiscograpy.
importTranscriptSequences
                        Incorporate manual transcript sequences into
                        the ProteoDiscography
incorporateGenomicVariants
                        Incorporate genomic events into their
                        overlapping exonic sequences
mutantTranscripts       Adds mutant transcript sequences to the
                        ProteoDiscography in the appropriate slot
ProteoDiscography-class
                        ProteoDiscography
ProteoDiscographyExample.hg19
                        Example ProteoDiscography.
setGenomicSequences     Change the underlying genomic sequences of a
                        ProteoDiscography object.
setMutantTranscripts    Adds mutant transcript sequences to the
                        ProteoDiscography in the appropriate slot
setTxDb                 Change the underlying TxDb of a
                        ProteoDiscography object.
