ICAMS (version 2.0.7)

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

Description

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

Usage

StrelkaIDVCFFilesToCatalogAndPlotToPdf(files, ref.genome,
  region = "unknown", 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.

output.file

The name of the PDF file to be produced.

Value

An ID (indel) catalog and its graph plotted to PDF with specified file name. The ID (indel) catalog has attributes added. See as.catalog for more details.

Details

This function calls StrelkaIDVCFFilesToCatalog and PlotCatalogToPdf

Examples

# NOT RUN {
file <- c(system.file("extdata",
                      "Strelka.ID.GRCh37.vcf",
                      package = "ICAMS"))
catID <- 
  StrelkaIDVCFFilesToCatalogAndPlotToPdf(file, ref.genome = "hg19", 
                                         region = "genome",
                                         output.file = file.path(tempdir(), 
                                                                 "StrelkaID.pdf"))
# }