ICAMS (version 2.1.2)

StrelkaSBSVCFFilesToCatalogAndPlotToPdf: Create SBS and DBS catalogs from Strelka SBS VCF files and plot them to PDF

Description

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

Usage

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

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

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 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) in files and file paths without extensions (and the leading dot) will be used as the names of the VCF files.

output.file

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

Value

A list of 3 SBS catalogs (one each for 96, 192, and 1536), 3 DBS catalogs (one each for 78, 136, and 144) and their graphs plotted to PDF with specified file name. If trans.ranges = NULL, 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 and PlotCatalogToPdf

Examples

# NOT RUN {
file <- c(system.file("extdata/Strelka-SBS-vcf",
                      "Strelka.SBS.GRCh37.s1.vcf",
                      package = "ICAMS"))
if (requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5", quietly = TRUE)) {
  catalogs <- 
    StrelkaSBSVCFFilesToCatalogAndPlotToPdf(file, ref.genome = "hg19",
                                            trans.ranges = trans.ranges.GRCh37,
                                            region = "genome",
                                            output.file = 
                                            file.path(tempdir(), "StrelkaSBS"))}
# }