ICAMS (version 2.0.10)

AnnotateDBSVCF: Add sequence context and transcript information to an in-memory DBS VCF.

Description

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

Usage

AnnotateDBSVCF(DBS.vcf, ref.genome, trans.ranges = NULL)

Arguments

DBS.vcf

An in-memory DBS VCF as a data.frame.

ref.genome

A ref.genome argument as described in ICAMS.

trans.ranges

a data.table which contains transcript range and strand information. Please refer to TranscriptRanges for more details. If is.null(trans.ranges) do not add transcript range information.

Value

An in-memory DBS 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.GRCh37.vcf",
                      package = "ICAMS"))
list.of.vcfs <- ReadAndSplitStrelkaSBSVCFs(file)
DBS.vcf <- list.of.vcfs$DBS.vcfs[[1]]             
if (requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5", quietly = TRUE)) {
  annotated.DBS.vcf <- AnnotateDBSVCF(DBS.vcf, ref.genome = "hg19",
                                      trans.ranges = trans.ranges.GRCh37)}
# }