ICAMS (version 2.0.10)

StrelkaSBSVCFFilesToCatalog: Create SBS and DBS catalogs from Strelka SBS VCF files.

Description

Create 3 SBS catalogs (96, 192, 1536) and 3 DBS catalogs (78, 136, 144) from the Strelka SBS VCFs specified by files

Usage

StrelkaSBSVCFFilesToCatalog(files, ref.genome, trans.ranges = NULL,
  region = "unknown", names.of.VCFs = NULL)

Arguments

files

Character vector of file paths to the Strelka SBS VCF files.

ref.genome

A ref.genome argument as described in ICAMS.

trans.ranges

a data.table which contains transcript range and strand information. Please refer to TranscriptRanges for more details.

region

A character string designating a genomic region; see as.catalog and ICAMS.

names.of.VCFs

Character vector of names of the VCF files. The order of names in names.of.VCFs should match the order of VCF file paths in files. If NULL(default), this function will remove all of the path up to and including the last path separator (if any) and file paths without extensions (and the leading dot) will be used as the names of the VCF files.

Value

A list of 3 SBS catalogs (one each for 96, 192, and 1536) and 3 DBS catalogs (one each for 78, 136, and 144). If trans.ranges = NULL, SBS 192 and 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.

Details

This function calls VCFsToSBSCatalogs and VCFsToDBSCatalogs.

Examples

# NOT RUN {
file <- c(system.file("extdata",
                      "Strelka.SBS.GRCh37.vcf",
                      package = "ICAMS"))
if (requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5", quietly = TRUE)) {
  catalogs <- StrelkaSBSVCFFilesToCatalog(file, ref.genome = "hg19",
                                          trans.ranges = trans.ranges.GRCh37,
                                          region = "genome")}
# }