sqlite.auto.build: Build annovarR database in sqlite (auto from...

In annovarR: Integrated Framework to Annotate Genetic Variants

Description

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

Usage

sqlite.auto.build(anno.name = "", buildver = "hg19",
  database.dir = "/path/", overwrite = FALSE, append = FALSE,
  index = "chr_start_index", db.type = "sqlite",
  database.cfg = system.file("extdata", "config/databases.toml", package =
  "annovarR"), extra_fread_params = list(sep = "\t", header = TRUE, return_1L
  = FALSE), sqlite.build.params = list(fread.params = list(sep = "\t")),
  batch_lines = 1e+07, start_index = 1, new.colnames = NULL,
  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
overwrite	Logical indicating wheather overwrite sqlite database, default is FALSE
append	Logical indicating wheather append the data to sqlite database, default is FALSE
index	Index name in sqlite
db.type	Setting the database type (sqlite, txt or mysql)
database.cfg	Configuration file of annovarR databases infomation
extra_fread_params	Pass to batch_file, default is to get value from database.cfg
sqlite.build.params	Extra params pass to sqlite.build
batch_lines	Parameters pass to batch_file, default is 10000000
start_index	default is 1, control the skip rows, n = (i-1) * batch_lines
new.colnames	Use the fread determined colnames or use new colnames
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)
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.