ICAMS (version 2.1.2)

MutectVCFFilesToZipFile: Create a zip file which contains catalogs and plot PDFs from Mutect VCF files

Description

Create 3 SBS catalogs (96, 192, 1536), 3 DBS catalogs (78, 136, 144) and Indel catalog from the Mutect VCFs specified by dir, save the catalogs as CSV files, plot them to PDF and generate a zip archive of all the output files.

Usage

MutectVCFFilesToZipFile(
  dir,
  zipfile,
  ref.genome,
  trans.ranges = NULL,
  region = "unknown",
  names.of.VCFs = NULL,
  tumor.col.names = NA,
  base.filename = "",
  flag.mismatches = 0
)

Arguments

dir

Pathname of the directory which contains the Mutect VCF files. Each Mutect VCF must have a file extension ".vcf" (case insensitive) and share the same ref.genome and region.

zipfile

Pathname of the zip file to be created.

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 VCFs listed in dir. If NULL(default), this function will remove all of the path up to and including the last path separator (if any) in dir and file paths without extensions (and the leading dot) will be used as the names of the VCF files.

tumor.col.names

Optional. Character vector of column names in VCFs which contain the tumor sample information. The order of names in tumor.col.names should match the order of VCFs listed in dir. If tumor.col.names is equal to NA(default), this function will use the 10th column in all the VCFs to calculate VAFs. See GetMutectVAF for more details.

base.filename

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

flag.mismatches

Optional. If > 0, then if there are mismatches to references in the ID (insertion/deletion) VCF, generate messages showing the mismatched rows and continue. Otherwise stop if there are mismatched rows. See AnnotateIDVCF for more details.

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 Indel catalog. 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 MutectVCFFilesToCatalog, PlotCatalogToPdf, WriteCatalog and zipr.

Examples

# NOT RUN {
dir <- c(system.file("extdata/Mutect-vcf",
                     package = "ICAMS"))
if (requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5", quietly = TRUE)) {
  catalogs <- 
    MutectVCFFilesToZipFile(dir, 
                            zipfile = file.path(tempdir(), "test.zip"),
                            ref.genome = "hg19", 
                            trans.ranges = trans.ranges.GRCh37,
                            region = "genome",
                            base.filename = "Mutect")
  unlink(file.path(tempdir(), "test.zip"))}
# }