ICAMS (version 2.1.2)

StrelkaSBSVCFFilesToZipFile: Create a zip file which contains catalogs and plot PDFs from Strelka SBS VCF files

Description

Create 3 SBS catalogs (96, 192, 1536), 3 DBS catalogs (78, 136, 144) from the Strelka SBS VCFs specified by dir, save the catalogs as CSV files, plot them to PDF and generate a zip archive of all the output files.

Usage

StrelkaSBSVCFFilesToZipFile(
  dir,
  zipfile,
  ref.genome,
  trans.ranges = NULL,
  region = "unknown",
  names.of.VCFs = NULL,
  base.filename = ""
)

Arguments

dir

Pathname of the directory which contains the Strelka SBS VCF files. Each Strelka SBS VCF must have a file extension ".vcf" (case insensitive) and share the same ref.genome and region.

zipfile

Pathname of the zip file to be created.

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.

names.of.VCFs

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

base.filename

Optional. The base name of the CSV and PDF files to be produced; multiple files will be generated, each ending in \(x\).csv or \(x\).pdf, where \(x\) indicates the type of catalog.

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 is not provided by user and cannot be inferred by ICAMS, then SBS 192 and DBS 144 catalog will not be generated and plotted. 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 StrelkaSBSVCFFilesToCatalog, PlotCatalogToPdf, WriteCatalog and zipr.

Examples

# NOT RUN {
dir <- c(system.file("extdata/Strelka-SBS-vcf",
                     package = "ICAMS"))
if (requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5", quietly = TRUE)) {
  catalogs <- 
    StrelkaSBSVCFFilesToZipFile(dir, 
                                zipfile = file.path(tempdir(), "test.zip"),
                                ref.genome = "hg19", 
                                trans.ranges = trans.ranges.GRCh37,
                                region = "genome",
                                base.filename = "Strelka-SBS")
  unlink(file.path(tempdir(), "test.zip"))}
# }