ICAMS (version 2.1.2)

AnnotateSBSVCF: 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)

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

1. BSgenome.Hsapiens.1000genomes.hs37d5

2. BSgenome.Hsapiens.UCSC.hg38

3. 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.

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

# NOT RUN {
file <- c(system.file("extdata/Strelka-SBS-vcf",
                      "Strelka.SBS.GRCh37.s1.vcf",
                      package = "ICAMS"))
list.of.vcfs <- ReadAndSplitStrelkaSBSVCFs(file)
SBS.vcf <- list.of.vcfs$SBS.vcfs[[1]]             
if (requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5", quietly = TRUE)) {
  annotated.SBS.vcf <- AnnotateSBSVCF(SBS.vcf, ref.genome = "hg19",
                                      trans.ranges = trans.ranges.GRCh37)}
# }