Add sequence context and transcript information to an in-memory SBS VCF
Add sequence context and transcript information to an in-memory SBS VCF
AnnotateSBSVCF(SBS.vcf, ref.genome, trans.ranges = NULL, name.of.VCF = NULL)
SBS.vcf |
An in-memory SBS VCF as a |
ref.genome |
A |
trans.ranges |
Optional. If
then the function will infer |
name.of.VCF |
Name of the VCF file. |
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).
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)}Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.