ICAMS (version 2.3.12)

VCFsToDBSCatalogs: Create DBS catalogs from VCFs

Description

Create a list of 3 catalogs (one each for DBS78, DBS144 and DBS136) out of the contents in list.of.DBS.vcfs. The VCFs must not contain any type of mutation other then DBSs.

Usage

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

Value

A list containing the following objects:

• catDBS78, catDBS136, catDBS144: Matrix of 3 DBS catalogs (one each for 78, 136, and 144).

• 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. DBS VCF annotated by AnnotateDBSVCF with three new columns DBS78.class, DBS136.class and DBS144.class showing the mutation class for each DBS variant.

If trans.ranges is not provided by user and cannot be inferred by ICAMS, DBS 144 catalog will not be generated. Each catalog has attributes added. See as.catalog for more details.

Arguments

list.of.DBS.vcfs

List of in-memory data frames of pure DBS mutations -- no SBS 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

1. BSgenome.Hsapiens.1000genomes.hs37d5

2. BSgenome.Hsapiens.UCSC.hg38

3. 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.

Comments

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

Examples

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