get_ott_lineage: Recursively get lineage from OTT taxid This function derives...

In alexpiper/taxreturn: An R package for retrieving and curating public DNA barcode reference data

Recursively get lineage from OTT taxid This function derives the full lineage of a taxon ID number from a given taxonomy database

Description

Recursively get lineage from OTT taxid This function derives the full lineage of a taxon ID number from a given taxonomy database

Usage

get_ott_lineage(
  x,
  db,
  output = "tax_name",
  ranks = c("kingdom", "phylum", "class", "order", "family", "genus", "species"),
  multithread = FALSE
)

Arguments

x	A DNAbin, DNAStringSet, taxonomy headers formnatted Acc|taxid;taxonomy, or vector of taxids
db	an OTT taxonomic database
output	Options are "tax_name" to return taxonomic names for each rank in the lineage or "tax_id" to return taxonomic ID's.
ranks	the taxonomic ranks to filter to. Default is "kingdom", "phylum", "class", "order", "family", "genus", "species" To get strain level ranks, add "terminal" to ranks
multithread	Whether multithreading should be used, if TRUE the number of cores will be automatically detected (Maximum available cores - 1), or provide a numeric vector to manually set the number of cores to use. Default is FALSE (single thread) This argument may alternatively be a 'cluster' object, in which case it is the user's responsibility to close the socket connection at the conclusion of the operation, for example by running parallel::stopCluster(cores).

alexpiper/taxreturn documentation built on Sept. 14, 2024, 7:56 p.m.