generateProteoDiscography: Generate the annotation database (ProteoDiscography)

In ErasmusMC-CCBC/ProteoDisco: Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences

Generate the annotation database (ProteoDiscography)

Description

Generates a database containing the genomic and transcriptomic annotations which will be used downstream to integrate genomic variants and discover mutant protein sequences with ProteoDisco.

By default, only the common seqlevels between the TxDb and genomeSeqs will be kept..

Usage

generateProteoDiscography(
  TxDb,
  genomeSeqs,
  useOnlySharedSeqlevels = TRUE,
  geneticCode = "Standard"
)

Arguments

TxDb	(TxDb): TxDb object containing the genomic and transcriptomic annotations.
genomeSeqs	(DNAStringSet or BSgenome): Genomic sequence of the respective genome.
useOnlySharedSeqlevels	(logical): Should only shared seqlevels between the TxDb and genomeSeqs be kept?
geneticCode	(character): Which codon-table should be used? Default is set to Standard, check GENETIC_CODE_TABLE for additional options.

Value

ProteoDiscography

Author(s)

Job van Riet [e-mail]

Wesley van de Geer [e-mail]

Examples

 # Generate a ProteoDiscography using existing TxDb and annotations.
 ProteoDiscography.hg19 <- ProteoDisco::generateProteoDiscography(
   TxDb = TxDb.Hsapiens.UCSC.hg19.knownGene::TxDb.Hsapiens.UCSC.hg19.knownGene, 
   genomeSeqs = BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19
 )
 

ErasmusMC-CCBC/ProteoDisco documentation built on Dec. 9, 2022, 8:41 a.m.