annovarR (version 1.0.0)

mysql.auto.index: Index annovarR database in mysql (auto from extdata/config/database.toml)

Description

Index annovarR database in mysql (auto from extdata/config/database.toml)

Usage

mysql.auto.index(anno.name = "", buildver = "hg19",
  database.dir = "/path/", mysql.connect.params = list(user = "", password =
  "", host = "localhost", port = "3306"), index = "chr_start_index",
  db.type = "mysql", database.cfg = system.file("extdata",
  "config/databases.toml", package = "annovarR"), verbose = TRUE)

Arguments

anno.name

Annotation name, eg. avsnp138, avsnp147, 1000g2015aug_all

buildver

Genome version, hg19, hg38, mm10 and others

database.dir

Dir of the databases (mysql no need)

mysql.connect.params

Mysql parameters, [host, dbname, table.name, user, password etc.]

index

Index name in sqlite

db.type

Setting the database type (sqlite, txt or mysql)

database.cfg

Configuration file of annovarR databases infomation

verbose

Logical indicating wheather print the extra log infomation

Examples

# NOT RUN {
i <- 'hg19_avsnp147'
database <- system.file('extdata', sprintf('demo/%s.txt', i), package = 'annovarR')
file.copy(database, sprintf('%s/%s.txt', tempdir(), i))
# }
# NOT RUN {
 mysql.auto.index(anno.name = 'avsnp147', database.dir = tempdir(), 
 mysql.connect.params = list(user = 'username', password = 'password', 
 host = 'localhost', port = 3306, dbname = 'annovarR'))
# }