sqlite.build: Build annovarR database in sqlite

In annovarR: Integrated Framework to Annotate Genetic Variants

Description

Build annovarR database in sqlite

Usage

sqlite.build(filename = NULL, sqlite.connect.params = list(dbname = "",
  table.name = ""), dat = data.table(), fread.params = list(),
  new.colnames = NULL, overwrite = TRUE, verbose = FALSE, ...)

Arguments

filename	Path of raw data, will be read by fread
sqlite.connect.params	Connect to sqlite database params [dbname, table.name]
dat	Object of data.table, as the input data to build database (optional)
fread.params	Other parameters be used in fread
new.colnames	New colnames of table, default is to retain the original
overwrite	Ligical indicating wheather overwrite sqlite database
verbose	Ligical indicating wheather show the log message
...	Other parameters be used in dbWriteTable

Examples

test.dat <- system.file('extdata', 'demo/sqlite.dat.txt', package = 'annovarR')
test.sqlite <- sprintf('%s/snp.test.sqlite', tempdir())
x <- sqlite.build(filename = test.dat, list(dbname = test.sqlite, 
table.name = 'snp_test'))
test.sqlite <- normalizePath(test.sqlite, '/')
file.remove(test.sqlite)

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