get_children: Get child nodes from NCBI taxonomy

View source: R/get_children.R

get_childrenR Documentation

Get child nodes from NCBI taxonomy

Description

This function will utilize a organism classification table to obtain all chidren species and/or strains with available NCBI reference sequences given a parent taxon and its rank.

Usage

get_children(input_taxon, input_rank, tax_dat = taxonomy_table)

Arguments

input_taxon

The parent taxon.

input_rank

The taxonomic rank of the input taxon.

tax_dat

A dataframe of organism classification information. At minimum, should have a column indicating "strain", and and all others should be taxonomic ranks. Each row should be a taxonomic relationship. This defaults to the 'taxonomy_table' object.

Value

Returns a vector of all the child species and/or strains of the input taxon.

Examples

## Get all child species and strains in bacteria superkingdom
get_children('Bacteria','superkingdom')

## Get all child species and strains in fungi kingdom
get_children('Fungi', 'kingdom')

## Get all child species in primate order
get_children('Primates', 'order')


compbiomed/MetaScope documentation built on Aug. 9, 2022, 10:41 a.m.