checkProteotypicFragments: Determine proteotypic fragments within the translated CDS

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

Determine proteotypic fragments within the translated CDS

Description

Proteotypic fragments are checked against the input TxDb (and additional peptide sequences) to infer whether peptide sequences contain one or multiple proteotypic fragment(s) after cleavage by a selected protease.

Usage

checkProteotypicFragments(
  x,
  enzymUsed = "trypsin",
  missedCleavages = 0,
  additionalPeptides = NULL,
  checkWithinMutantSeqs = FALSE
)

## S4 method for signature 'ProteoDiscography'
checkProteotypicFragments(
  x,
  enzymUsed = "Trypsin",
  missedCleavages = 0,
  additionalPeptides = NULL,
  checkWithinMutantSeqs = FALSE
)

Arguments

x	(ProteoDiscography): ProteoDiscography object which stores the annotation and genomic sequences.
enzymUsed	(character): Preferred proteasome used in cleaving the peptide sequences, e.g. trypsin.
missedCleavages	(integer): Number of subsequent missed cleavages.
additionalPeptides	(AAStringSet): Additional peptide sequences against which to check proteotypic fragments, besides the input TxDb. If left empty, only the (translated) input TxDb will be checked.
checkWithinMutantSeqs	(logical): Should proteotypic fragments also not be present within another mutant peptide-sequence?

Value

ProteoDiscography with additional information added to the transcript sequence information.

ProteoDiscography with an additional column specifying the number of proteotypic fragments per record.

Author(s)

Job van Riet [e-mail]

Wesley van de Geer [e-mail]

Examples

# Import example ProteoDiscography (hg19)
data('ProteoDiscographyExample.hg19', package = 'ProteoDisco')
ProteoDiscographyExample.hg19 <- setTxDb(ProteoDiscographyExample.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene::TxDb.Hsapiens.UCSC.hg19.knownGene)
ProteoDiscographyExample.hg19 <- setGenomicSequences(ProteoDiscographyExample.hg19, BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19)

# Results will now contain additional information about proteotypic fragments.
# With a large TxDb, this can take a while.
# ProteoDiscography.hg19 <- ProteoDisco::checkProteotypicFragments(ProteoDiscographyExample.hg19)

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