importGenomicVariants: Import genomic variants into the ProteoDiscography

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

Import genomic variants into the ProteoDiscography

Description

Imports genomic variants (SNV, MNV and InDels) present within the supplied VCF/MAF files into the ProteoDiscography as a VRanges. This genomic variants can later be incorporated within transcript sequences at a later stage.

Usage

importGenomicVariants(
  ProteoDiscography,
  files,
  samplenames = NULL,
  removeExisting = FALSE,
  overwriteDuplicateSamples = TRUE,
  performAnchorCheck = TRUE,
  ignoreNonMatch = FALSE,
  threads = 1
)

Arguments

ProteoDiscography	(ProteoDiscography): ProteoDiscography object which stores the annotation and genomic sequences.
files	(character): Path(s) to VCF or MAF files.
samplenames	(character): Descriptive samplename(s) of the VCF files in the same order as input VCF file(s), if NULL the basename of the file will be used instead.
removeExisting	(logical): Should previous mutations within the ProteoDiscography be removed?
overwriteDuplicateSamples	(logical): Replace duplicate samples (TRUE) or throw an error if duplicate samples are found.
performAnchorCheck	(logical): Should the reference anchor be check for consistency with the given genomic sequences?
ignoreNonMatch	(logical): Should non-matching reference anchors be ignored? These mutations will be removed prior to appending.
threads	(integer): Number of threads.

Value

ProteoDiscography with additional imported SNVs, MNVs and InDels.

Author(s)

Job van Riet [e-mail]

Wesley van de Geer [e-mail]

Examples

ProteoDiscography.hg19 <- ProteoDisco::generateProteoDiscography(
  TxDb = TxDb.Hsapiens.UCSC.hg19.knownGene::TxDb.Hsapiens.UCSC.hg19.knownGene, 
  genomeSeqs = BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19
)

# Supply the ProteoDiscography with genomic variants to incorporate in downstream analysis. This can be one or multiple VCF / MAF files.
# Additional manual sequences and exon-exon mapping (i.e., splice junctions) can also be given as shown in the sections below.
ProteoDiscography.hg19 <- ProteoDisco::importGenomicVariants(
  ProteoDiscography = ProteoDiscography.hg19,
  # Provide the VCF / MAF files, if more then one supply a vector of files and corresponding samplenames.
  files = system.file('extdata', 'validationSet_hg19.vcf', package = 'ProteoDisco'), 
  # We can replace the original samples within the VCF with nicer names.
  samplenames = 'Validation Set (GRCh37)',
  # Number of threads used for parallelization.
  # We run samples sequentially and parallelize within (variant-wise multi-threading).
  threads = 1, 
  # To increase import-speed for this example, do not check for validity of the reference anchor with the given reference sequences.
  performAnchorCheck = FALSE
)
 

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