AnnotateIDVCFsWithTransRanges: Add sequence context and transcript information to an...
In steverozen/ICAMSxtra: ICAMSxtra

Description Usage Arguments Value Examples

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

AnnotateIDVCFsWithTransRanges(
  ID.vcfs,
  ref.genome,
  trans.ranges = NULL,
  vcf.names = NULL
)

`ID.vcfs`	A list of in-memory ID 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.
`vcf.names`	list of names of the vcfs

A list of in-memory ID VCFs each a data.table. These have been annotated with the sequence context (column name seq.context) 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-ID-vcf",
                      "Strelka.ID.GRCh37.s1.vcf",
                      package = "ICAMSxtra"))
list.of.vcfs <- ICAMS::ReadAndSplitVCFs(file, variant.caller = "strelka")$ID
if (requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5", quietly = TRUE)) {
  annotated.ID.vcfs <- AnnotateIDVCFsWithTransRanges(list.of.vcfs, ref.genome = "hg19",
                                                    trans.ranges = ICAMS::trans.ranges.GRCh37)
  }