ICAMS (version 2.0.8)

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", 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

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.

output.file

The name of the PDF file to be produced.

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.

Details

This function calls StrelkaSBSVCFFilesToCatalog and PlotCatalogToPdf

Examples

# NOT RUN {
file <- c(system.file("extdata",
                      "Strelka.SBS.GRCh37.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.pdf"))}
                                                                    
# }