VCFsToSBSCatalogs: Create SBS catalogs from SBS VCFs
In ICAMS: In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')

Description Usage Arguments Value Comments Note Examples

View source: R/shiny_related_functions.R

Create a list of 3 catalogs (one each for 96, 192, 1536) out of the contents in list.of.SBS.vcfs. The SBS VCFs must not contain DBSs, indels, or other types of mutations.

VCFsToSBSCatalogs(
  list.of.SBS.vcfs,
  ref.genome,
  num.of.cores = 1,
  trans.ranges = NULL,
  region = "unknown",
  return.annotated.vcfs = FALSE,
  suppress.discarded.variants.warnings = TRUE
)

`list.of.SBS.vcfs`	List of in-memory data frames of pure SBS mutations – no DBS or 3+BS mutations. The list names will be the sample ids in the output catalog.
`ref.genome`	A `ref.genome` argument as described in `ICAMS`.
`num.of.cores`	The number of cores to use. Not available on Windows unless `num.of.cores = 1`.
`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.
`region`	A character string designating a genomic region; see `as.catalog` and `ICAMS`.
`return.annotated.vcfs`	Logical. Whether to return the annotated VCFs with additional columns showing mutation class for each variant. Default is FALSE.
`suppress.discarded.variants.warnings`	Logical. Whether to suppress warning messages showing information about the discarded variants. Default is TRUE.

A list containing the following objects:

catSBS96, catSBS192, catSBS1536: Matrix of 3 SBS catalogs (one each for 96, 192, and 1536).
discarded.variants: Non-NULL only if there are variants that were excluded from the analysis. See the added extra column discarded.reason for more details.
annotated.vcfs: Non-NULL only if return.annotated.vcfs = TRUE. SBS VCF annotated by AnnotateSBSVCF with three new columns SBS96.class, SBS192.class and SBS1536.class showing the mutation class for each SBS variant.

If trans.ranges is not provided by user and cannot be inferred by ICAMS, SBS 192 catalog will not be generated. Each catalog has attributes added. See as.catalog for more details.

To add or change attributes of the catalog, you can use function attr.
For example, attr(catalog, "abundance") <- custom.abundance.

SBS 192 catalogs only contain mutations in transcribed regions.

file <- c(system.file("extdata/Mutect-vcf",
                      "Mutect.GRCh37.s1.vcf",
                      package = "ICAMS"))
list.of.SBS.vcfs <- ReadAndSplitMutectVCFs(file)$SBS
if (requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5", quietly = TRUE)) {
  catalogs.SBS <- VCFsToSBSCatalogs(list.of.SBS.vcfs, ref.genome = "hg19",
                                    trans.ranges = trans.ranges.GRCh37,
                                    region = "genome")}