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


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Documentation for package ‘ProteoDisco’ version 1.4.0

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.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.