prune_taxonomy: Prune taxonomy database.

In insect: Informatic Sequence Classification Trees

Description

This function prunes the taxon database, removing specified taxa as desired to improve speed and memory efficiency.

Usage

prune_taxonomy(db, taxIDs, keep = TRUE)

Arguments

db	a valid taxonomy database, e.g. obtained by running the taxonomy function.
taxIDs	the names or taxon ID numbers of the taxa to be retained (or discarded if keep = FALSE).
keep	logical, indicates whether the specified taxa should be kept and the rest of the database removed or vice versa. Defaults to TRUE.

Details

TBA

Value

a data.frame with the same column names as the input object ("taxID", "parent_taxID", "rank", "name").

Author(s)

Shaun Wilkinson

References

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/

Examples

## remove Odontoceti suborder from cetacean taxonomy database
data(whale_taxonomy)
prune_taxonomy(whale_taxonomy, taxIDs = 9722, keep = FALSE)

insect documentation built on Aug. 9, 2021, 5:07 p.m.