sqlite.auto.index: Index annovarR database in sqlite (auto from...

In annovarR: Integrated Framework to Annotate Genetic Variants

Description

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

Usage

sqlite.auto.index(anno.name = "", buildver = "hg19",
  database.dir = "/path/", index = "chr_start_index", db.type = "sqlite",
  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
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

i <- 'hg19_avsnp147'
database <- system.file('extdata', sprintf('demo/%s.txt', i), package = 'annovarR')
file.copy(database, sprintf('%s/%s.txt', tempdir(), i))
sqlite.auto.build('avsnp147', 'hg19', database.dir = tempdir(), verbose = TRUE)
sqlite.auto.index('avsnp147', 'hg19', database.dir = tempdir(), index = 'chr_start_index2',
verbose = TRUE)
unlink(sprintf('%s/%s.txt', tempdir(), i))
unlink(sprintf('%s/%s.sqlite', tempdir(), i))

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