incorporateGenomicVariants: Incorporate genomic events into their overlapping exonic...

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

Incorporate genomic events into their overlapping exonic sequences

Description

incorporateMutations Incorporates SNV, MNV and InDels present in the ProteoDiscography on the transcripts.

Usage

incorporateGenomicVariants(
  ProteoDiscography,
  aggregateSamples = FALSE,
  aggregateWithinExon = TRUE,
  aggregateWithinTranscript = TRUE,
  ignoreOverlappingMutations = TRUE,
  threads = 1
)

Arguments

ProteoDiscography	(ProteoDiscography): ProteoDiscography object which stores the annotation and genomic sequences.
aggregateSamples	(logical): Should genomic mutations from different samples be incorporated within the same transcript?
aggregateWithinExon	(logical): Should multiple mutations within the same exon be aggregated (TRUE) or should each mutation per exon produce a separate mutant transcript?
aggregateWithinTranscript	(logical): Should multiple mutant exons within the same transcript be aggregated?
ignoreOverlappingMutations	(logical): Incorporate first mutation (by order) and ignore subsequent overlapping mutations (and provide a warning) or stop the incorporation (if set to TRUE). If aggregateWithinExon is set to FALSE, each mutations are added into separate exon to produce seperate transcripts.
threads	(integer): Number of threads.

Value

ProteoDiscography with mutant transcript sequences containing SNVs, MNVs and InDels.

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)

# Incorporate the genomic variants.
ProteoDiscographyExample.hg19 <- ProteoDisco::incorporateGenomicVariants(
  ProteoDiscography = ProteoDiscographyExample.hg19,
  # Do not aggregate samples and generate mutant transcripts from the mutations per sample.
  aggregateSamples = FALSE,
  # If there are multiple mutations within the same exon (CDS), place them on the same mutant CDS sequence.
  aggregateWithinExon = TRUE,
  # Aggregate multiple mutant exons (CDS) within the same transcripts instead of incorporating one at a time.
  aggregateWithinTranscript = TRUE,
  # If there are overlapping mutations on the same coding position, retain only the first of the overlapping mutations.
  # If set to FALSE, throw an error and specify which CDS had overlapping mutations.
  ignoreOverlappingMutations = TRUE,
  # Number of threads.
  threads = 1
)

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