mysql.auto.index: Index anor database in mysql (auto from...

In JhuangLab/annovarR: Integrated Framework to Annotate Genetic Variants

Description

Index anor 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 = "anor"),
  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 anor databases infomation
verbose	Logical indicating wheather print the extra log infomation

Examples

i <- 'hg19_avsnp147'
database <- system.file('extdata', sprintf('demo/%s.txt', i), package = 'anor')
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 = 'anor'))

## End(Not run)

JhuangLab/annovarR documentation built on April 23, 2020, 10:51 p.m.