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

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Documentation for package ‘ProteoDisco’ version 1.15.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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.