taxon-constructors: Retrieve records from the NCBI Taxonomy database (locally or...

In gschofl/ncbi: Retrieve data from NCBI.

Description

Retrieve records from the NCBI Taxonomy database (locally or remote)

Usage

  taxon(taxid, rettype = NULL, retmax = 25, parse = TRUE,
    ...)

  taxonDB(taxid, full = TRUE, ...)

  taxonByGeneID(geneid, full = TRUE, ...)

Arguments

taxid	‘taxids’ or a valid NCBI search term.
rettype	Which type of data should be retrieved? Full records (default: NULL) or an ‘uilist’.
retmax	Maximal number of records to be retrieved (default: 25).
parse	Should the retrieved data be parsed?
...	Parameters passed on to the underlying efetch query.
taxid	A vector of valid NCBI Taxonomy Identifiers.
full	if FALSE a minimal taxonomic description is extracted (TaxId, ScientificName, Rank).
...
geneid	A vector of valid NCBI Gene Identifiers.

Details

taxonDB and taxonByGeneID require a local installation of the NCBI taxonomy database and a database providing the GI to TaxId mapping. These databases are created using createTaxonDB and createGeneidDB, respectively, and kept up to date with updateTaxonDB and updateGeneidDB.

The install path for these custom databases taxon.db and geneid.db is specified by setting the global option ncbi.taxonomy.path. Currently, it defaults to "$HOME/local/db/taxonomy/". The default path can be overridden permanently by setting this option in the .Rprofile file.

Note that the geneid.db file can get fairly large (currently ~6GB) and takes a long time to create.

See the documentation at NCBI for more information on the NCBI Taxonomy database.

Value

An XMLInternalDocument or if parsed a Taxon or TaxonList instance.

See Also

createTaxonDB, updateTaxonDB

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