This function retrieves category information from NCBI Taxonomy and is able to filter kingdom specific taxids.
Arguments
- db.path
path to download and store the NCBI Taxonomy
categories.dmp
file. Default is thetempdir()
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 thedb.path
argument to target the localcategories.dmp
file).- update
should the local file be updated? Please specify the
db.path
argument to target the localcategories.dmp
file.- filter
a character string specifying the kingdom of life for which taxids shall be returned. Options are
"Archea"
,"Bacteria"
,"Eukaryota"
,"Viruses"
,"Unclassified"
.
Examples
if (FALSE) { # \dontrun{
# 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")
} # }