get_children: Get child nodes from NCBI taxonomy

In compbiomed/MetaScope: Tools and functions for preprocessing 16S and metagenomic sequencing microbiome data

Get child nodes from NCBI taxonomy

Description

This function will utilize an organism classification table to obtain all children 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 = NULL)

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 NULL, which calls 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 Nov. 5, 2024, 9:25 p.m.