GenerateZipFileFromVCFs: This function generates a zip archive from VCFs

In steverozen/mSigAct.server: Shiny Server for Analyzing Mutational Signature Activities

This function generates a zip archive from VCFs

Description

This function generates a zip archive from VCFs

Usage

GenerateZipFileFromVCFs(
  files,
  zipfile,
  vcf.names,
  zipfile.name,
  ref.genome,
  variant.caller,
  mergeSBS,
  filter.status,
  num.of.cores,
  trans.ranges = NULL,
  region = "unknown",
  names.of.VCFs = NULL,
  base.filename = "",
  updateProgress = NULL
)

Arguments

files	Character vector of file paths to the VCF files.
zipfile	Pathname of the zip file to be created.
vcf.names	Names of VCF files uploaded by the user.
zipfile.name	Name of zip archive specified by the user.
ref.genome	A ref.genome argument as described in ICAMS.
variant.caller	Name of the variant caller that produces the VCF, can be either strelka, mutect or freebayes. This information is needed to calculate the VAFs (variant allele frequencies). If "unknown"(default) and get.vaf.function is NULL, then VAF and read depth will be NAs.
mergeSBS	Whether to merge adjacent SBSs as DBS. Value can be "yes" or "no".
filter.status	The character string in column FILTER of the VCF that indicates that a variant has passed all the variant caller's filters.
num.of.cores	The number of cores to use. Not available on Windows unless num.of.cores = 1.
trans.ranges	Optional. If ref.genome specifies one of the BSgenome object BSgenome.Hsapiens.1000genomes.hs37d5 BSgenome.Hsapiens.UCSC.hg38 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 files. If NULL(default), this function will remove all of the path up to and including the last path separator (if any) in files and file paths without extensions (and the leading dot) will be used as the names of the VCF files.
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.
updateProgress	A callback function to update the progress indicator on the user interface.

steverozen/mSigAct.server documentation built on July 9, 2023, 4:52 a.m.