getTaxonomy: Get the Taxonomic tree function

Description Usage Arguments Value Examples

View source: R/getTaxonomy.R

Description

The function to obtain the taxonomic tree from the database in the newick format that can be plugged into phylo.io for visualisation.

Usage

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getTaxonomy(root = NULL, members = NULL, newick = TRUE)

Arguments

root

optional parameter, the root of the node of interest

members

optional parameter, list of member ncbi taxon or UniProt IDs that should be included in the induced taxonomy.

newick

optional parameter, boolean default set to TRUE

Value

an object containing the JSON keys as attributes

Examples

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getTaxonomy()
getTaxonomy(members='YEAST,ASHGO')
getTaxonomy(root='Alveolata')

klarakaleb/roma documentation built on Nov. 11, 2020, 5:36 a.m.