Description Usage Arguments Details Value Author(s) References Examples
This function prunes the taxon database, removing specified taxa as desired to improve speed and memory efficiency.
1 | prune_taxonomy(db, taxIDs, keep = TRUE)
|
db |
a valid taxonomy database, e.g. obtained by running the
|
taxIDs |
the names or taxon ID numbers of the taxa to be retained
(or discarded if |
keep |
logical, indicates whether the specified taxa should be kept and the rest of the database removed or vice versa. Defaults to TRUE. |
TBA
a data.frame with the same column names as the input object ("taxID", "parent_taxID", "rank", "name").
Shaun Wilkinson
Federhen S (2012) The NCBI Taxonomy database. Nucleic Acids Research 40, D136-D143. doi:10.1093/nar/gkr1178.
https://www.ncbi.nlm.nih.gov/taxonomy/
1 2 3 | ## remove Odontoceti suborder from cetacean taxonomy database
data(whale_taxonomy)
prune_taxonomy(whale_taxonomy, taxIDs = 9722, keep = FALSE)
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