{taxonomy_kit} R# Documentation

taxonomy_kit


require(GCModeller);

#' toolkit for process ncbi taxonomy tree data
imports "taxonomy_kit" from "metagenomics_kit";

toolkit for process ncbi taxonomy tree data

The Taxonomy Database is a curated classification and nomenclature for all of the organisms in the public sequence databases. This currently represents about 10% of the described species of life on the planet.

.NET clr type export
taxonomy: Taxonomy

A simple organism taxonomy model.



.NET clr function exports
biom.string

cast taxonomy object to biom style taxonomy string

biom_string.parse

parse the taxonomy string in BIOM style

unique_taxonomy

make taxonomy object unique

Ncbi.taxonomy_tree

load ncbi taxonomy tree model from the given data files

ranks

cast the ncbi taxonomy tree model to taxonomy ranks data

taxonomy_ranks

get all taxonomy tree nodes of the specific taxonomy ranks

taxonomy.filter
lineage

get taxonomy lineage model from the ncbi taxonomy tree by given taxonomy id

as.taxonomy.tree

build taxonomy tree based on a given collection of taxonomy object.

consensus
read.mothurTree

Parse the result output from mothur command summary.tax.

as.OTU_table

convert the mothur rank tree as the OTU table

read.OTUtable

read 16s OTU table

taxonomy_range

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