Retrieve taxonomy categories from NCBI Taxonomy

This function retrieves category information from NCBI Taxonomy and is able to filter kingdom specific taxids.

Usage

taxid(db.path, download = FALSE, update = FALSE, filter = NULL)

Arguments

db.path: path to download and store the NCBI Taxonomy categories.dmp file. Default is the tempdir() directory.
download: a logical value specifying whether or not the categories.dmp shall be downloaded (download = TRUE) or whether a local version already exists on the users machine (download = TRUE - in this case please specify the db.path argument to target the local categories.dmp file).
update: should the local file be updated? Please specify the db.path argument to target the local categories.dmp file.
filter: a character string specifying the kingdom of life for which taxids shall be returned. Options are "Archea", "Bacteria", "Eukaryota", "Viruses", "Unclassified".

Value

A tibble object containing taxonomy category information

Author

Hajk-Georg Drost

Examples

if (FALSE) {
# download categories.dmp file to current working directory 
# and filter for 'Archea' taxids
Archea.taxids <- taxid(db.path = getwd(), filter = "Archea", download = TRUE)

# Once the NCBI Taxonomy 'categories.dmp' file is downloaded to your machine ('download = TRUE')
# the 'taxid()' function can be proceed on the local 'categories.dmp' file
# e.g. filter for Virus taxids
Virus.taxids <- taxid(db.path = getwd(), filter = "Viruses")
}