annovarR (version 1.0.0)

download.database: Download annovarR databases

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

# NOT RUN {
download.database('db_annovar_avsnp', database.dir = sprintf('%s/databases/', tempdir()), 
show.all.versions = TRUE)
# }