Retrieve taxonomy categories from NCBI Taxonomy

Source: R/taxid.R

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

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".

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")
}