subset_clade: Subset the taxonomy tree from the root

In larssnip/microclass: Tools for taxonomic classification of prokaryotes

Subset the taxonomy tree from the root

Description

Retrieves a clade from the taxonomy tree.

Usage

subset_clade(root.tax.id, nodes.dmp)

Arguments

root.tax.id	the tax_id of the clade root (integer).
nodes.dmp	a nodes.dmp table.

Details

This function retrieves a clade from the taxonomy tree listed in the table nodes.dmp (see read_nodes_dmp). The clade starts at the single taxon specified in root_tax_id and contains all descending branches.

If you want to subset the taxonomy tree based on leaf nodes, see subset_tree.

Value

A subset of the table nodes.dmp containing the clade that descends from root.tax.id.

Author(s)

Lars Snipen.

See Also

read_nodes_dmp, subset_tree.

larssnip/microclass documentation built on Nov. 1, 2023, 2:39 p.m.