ICAMS (version 2.1.2)

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

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.

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 DBS catalogs, one each for 78, 144, 136: catDBS78 catDBS144 catDBS136. 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.

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.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")}
# }