ICAMS (version 2.3.12)

VCFsToSBSCatalogs: Create SBS catalogs from SBS VCFs

Description

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.

Usage

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
)

Value

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.

Arguments

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

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.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")}