refdb_import_BOLD: Download and import BOLD records

In refdb: A DNA Reference Library Manager

Download and import BOLD records

Description

This function allows to search and download data from the the BOLD database. Additionally it allows to convert the BOLD taxonomic classification into the NCBI classification using the NCBI Taxonomy database.

Usage

refdb_import_BOLD(
  taxon = NULL,
  ids = NULL,
  bin = NULL,
  container = NULL,
  institutions = NULL,
  researchers = NULL,
  geo = NULL,
  ncbi_taxo = TRUE,
  full = FALSE,
  verbose = TRUE
)

Arguments

taxon, ids, bin, container, institutions, researchers, geo	terms used to search the BOLD database. See bold_seqspec from which they are inherited.
ncbi_taxo	if TRUE (the default) the BOLD taxonomy is replaced by the NCBI taxonomy using refdb_set_ncbitax.
full	if TRUE the complete data are returned for every records. If FALSE (the default) only a subset of the most important columns is returned.
verbose	print information in the console.

Details

This function uses several functions of the bold package to interface with the BOLD API. The NCBI Taxonomy database is queried using the rentrez package.

Value

A tibble.

Large requests

As detailed in the manual of bold_seqspec, some large requests (e.g. high ranked taxa) can lead to errors. In that case one strategy can be to sequentially download data for lower rank taxa. See https://docs.ropensci.org/bold/#large-data.

See Also

link[bold]bold_stats and bold_seqspec from bold which are used internally.

Examples

## Not run: 
goera_bold <- refdb_import_BOLD(taxon = "Goera pilosa", ncbi_taxo = FALSE)

## End(Not run)

refdb documentation built on Sept. 22, 2022, 5:07 p.m.