ICAMS (version 2.0.10)

StrelkaIDVCFFilesToCatalogAndPlotToPdf: Create ID (small insertion and deletion) catalog from Strelka ID VCF files and plot them to PDF

Description

Create ID (small insertion and deletion) catalog from the Strelka ID VCFs specified by files and plot them to PDF

Usage

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

Arguments

files

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

ref.genome

A ref.genome argument as described in ICAMS.

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.

output.file

The base name of the PDF file to be produced; the file is ending in catID.pdf.

Value

A list whose first element is an ID (small insertion and deletion) catalog with its graph plotted to PDF with specified file name. The ID catalog has attributes added. See as.catalog for more details. The second element of the returned list is a list of further annotated VCFs.

Details

This function calls StrelkaIDVCFFilesToCatalog and PlotCatalogToPdf

Examples

# NOT RUN {
file <- c(system.file("extdata",
                      "Strelka.ID.GRCh37.vcf",
                      package = "ICAMS"))
if (requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5", quietly = TRUE)) {
  catID <- 
    StrelkaIDVCFFilesToCatalogAndPlotToPdf(file, ref.genome = "hg19", 
                                           region = "genome",
                                           output.file = 
                                           file.path(tempdir(), "StrelkaID"))}
                                                                   
# }