download.database: Download annovarR databases

In annovarR: Integrated Framework to Annotate Genetic Variants

Description

Download annovarR databases

Usage

download.database(download.name = NULL, database.dir = tempdir(),
  version = c(), buildver = "hg19", download.cfg = system.file("extdata",
  "config/db/db_annovar.toml", package = "BioInstaller"),
  show.all.versions = FALSE, show.all.names = FALSE,
  show.all.buildvers = FALSE, verbose = FALSE, ...)

Arguments

download.name	Download name, default is NULL and get value from database.cfg dependence_db
database.dir	Destination directory to store databases
version	Version of download database, supported version can be get by download.database('db_annovar_avsnp', show.all.versions = TRUE)
buildver	Genome version, e.g hg19, hg38, mm10
download.cfg	Configuration file for download, most of annovarR database resources can be found in system.file('extdata', 'config/db/db_annovar.toml', package = 'BioInstaller')
show.all.versions	Logical indicating wheather show all avaliable versions
show.all.names	Logical indicating wheather show all avaliable name
show.all.buildvers	Logical indicating wheather show all avaliable buildver
verbose	Logical indicating wheather print the extra log infomation
...	Other parameters pass to install.bioinfo

Examples

download.database('db_annovar_avsnp', database.dir = sprintf('%s/databases/', tempdir()), 
show.all.versions = TRUE)

annovarR documentation built on Jan. 9, 2018, 5:05 p.m.