AnnotateDBSVCF: Add sequence context and transcript information to an...
In ICAMS: In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')

Description Usage Arguments Value Examples

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

1	AnnotateDBSVCF(DBS.vcf, ref.genome, trans.ranges = NULL, name.of.VCF = NULL)

`DBS.vcf`	An in-memory DBS 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.

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).

file <- c(system.file("extdata/Strelka-SBS-vcf",
                      "Strelka.SBS.GRCh37.s1.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)}