Description Usage Arguments Examples
Index annovarR database in mysql (auto from extdata/config/database.toml)
1 2 3 4 5 | 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)
|
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 |
1 2 3 4 5 6 7 8 9 | 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'))
## End(Not run)
|
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