R: Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences

# Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences

## Documentation for package ‘ProteoDisco’ version 1.18.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

.checkReferenceAnchor | Checks if mutations and reference genome correspond
checkProteotypicFragments | Determine proteotypic fragments within the translated CDS
checkProteotypicFragments-method | 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.
getDiscography-method | 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
mutantTranscripts-method | 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.
setGenomicSequences-method | Change the underlying genomic sequences of a ProteoDiscography object.
setMutantTranscripts | Adds mutant transcript sequences to the ProteoDiscography in the appropriate slot
setMutantTranscripts-method | Adds mutant transcript sequences to the ProteoDiscography in the appropriate slot
setTxDb | Change the underlying TxDb of a ProteoDiscography object.
setTxDb-method | Change the underlying TxDb of a ProteoDiscography object.