AnnotateSBSVCF: Add sequence context and transcript information to an...

In ICAMS: In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')

Add sequence context and transcript information to an in-memory SBS VCF

Description

Add sequence context and transcript information to an in-memory SBS VCF

Usage

AnnotateSBSVCF(SBS.vcf, ref.genome, trans.ranges = NULL, name.of.VCF = NULL)

Arguments

SBS.vcf	An in-memory SBS VCF as a data.frame.
ref.genome	A ref.genome argument as described in ICAMS.
trans.ranges	Optional. If ref.genome specifies one of the BSgenome object BSgenome.Hsapiens.1000genomes.hs37d5 BSgenome.Hsapiens.UCSC.hg38 BSgenome.Mmusculus.UCSC.mm10 then the function will infer trans.ranges automatically. Otherwise, user will need to provide the necessary trans.ranges. Please refer to TranscriptRanges for more details. If is.null(trans.ranges) do not add transcript range information.
name.of.VCF	Name of the VCF file.

Value

An in-memory SBS VCF as a data.table. This has been annotated with the sequence context (column name seq.21bases) and with transcript information in the form of a gene symbol (e.g. "TP53") and transcript strand. This information is in the columns trans.start.pos, trans.end.pos , trans.strand, trans.Ensembl.gene.ID and trans.gene.symbol in the output. These columns are not added if is.null(trans.ranges).

Examples

file <- c(system.file("extdata/Strelka-SBS-vcf",
                      "Strelka.SBS.GRCh37.s1.vcf",
                      package = "ICAMS"))
list.of.vcfs <- ReadAndSplitVCFs(file, variant.caller = "strelka")
SBS.vcf <- list.of.vcfs$SBS[[1]]
if (requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5", quietly = TRUE)) {
  annotated.SBS.vcf <- AnnotateSBSVCF(SBS.vcf, ref.genome = "hg19",
                                      trans.ranges = trans.ranges.GRCh37)}

ICAMS documentation built on June 15, 2025, 1:08 a.m.