mgigenes_gz2sql: Convert gzipped file of MGI genes to SQLite database

In byandell/CCSanger: Utilities to get and use Sanger data for Collaborative Cross

Description

Read file, filter to MGI identified genes and copy to database. If database does not exist, create it. The gzipped gene file is 24.8Mb,or 368.2Mb uncompressed. The R object with only type=="gene" and known Name is 10.5Mb. Storing in SQLite, file is 1.5Mb.

Usage

mgigenes_gz2sql(gene_tbl = "mgi_gene", sql_file = "mgi_db.sqlite",
  gz_file = file.path("ftp://ftp.jax.org", "SNPtools", "genes",
  "MGI.20130703.sorted.txt.gz"))

Arguments

gene_tbl	character string of tbl to be used in database
sql_file	character string name of SQLite file
gz_file	character string path to MGI gene file

Value

tbl collected from SQLite database (invisible)

Examples

dontrun(mgigenes_gz2sql("mgi_gene"))

byandell/CCSanger documentation built on May 13, 2019, 9:26 a.m.