ICAMS (version 2.1.2)

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,
  trans.ranges = NULL,
  region = "unknown"
)

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.

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.

Value

A list of 3 SBS catalogs, one each for 96, 192, 1536: catSBS96 catSBS192 catSBS1536. 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.

Comments

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

Examples

# NOT RUN {
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")}
# }