ICAMS (version 2.0.7)

MutectVCFFilesToCatalogAndPlotToPdf: Create SBS, DBS and Indel catalogs from Mutect VCF files and plot them to PDF

Description

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

Usage

MutectVCFFilesToCatalogAndPlotToPdf(files, ref.genome,
  trans.ranges = NULL, region = "unknown", output.file)

Arguments

files

Character vector of file paths to the Mutect 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), Indel catalog 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 MutectVCFFilesToCatalog and PlotCatalogToPdf

Examples

# NOT RUN {
file <- c(system.file("extdata",
                      "Mutect.GRCh37.vcf",
                      package = "ICAMS"))
catalogs <- 
  MutectVCFFilesToCatalogAndPlotToPdf(file, ref.genome = "hg19", 
                                      trans.ranges = trans.ranges.GRCh37,
                                      region = "genome",
                                      output.file = file.path(tempdir(), "Mutect.pdf"))
# }