TaxonDB: Create a local install of the NCBI Taxonomy database.

In gschofl/ncbi: Retrieve data from NCBI.

Description

Create a local install of the NCBI Taxonomy database.

Usage

  createTaxonDB(db_path = getOption("ncbi.taxonomy.path"))

  updateTaxonDB(db_path = getOption("ncbi.taxonomy.path"))

  createGeneidDB(db_path = getOption("ncbi.taxonomy.path"))

  updateGeneidDB(db_path = getOption("ncbi.taxonomy.path"))

Arguments

db_path

Parent directory for SQLite database files.

Details

From the commandline run: R -q -e "require(ncbi);createTaxonDB();createGeneidDB()"

This will install two SQLite databases "taxon.db" and "geneid.db" in "$HOME/local/db/taxonomy/". To override the default installation directory set the option ncbi.taxonomy.path in your .Rprofile.

See Also

taxonDBConnect, geneidDBConnect

gschofl/ncbi documentation built on May 17, 2019, 8:53 a.m.