assign_hierarchy

Assigns hierarchy metadata to a metabolomics count matrix using identifier values.
It can assign KEGG compound hierarchy, orthology hierarchy, or organism hierarchy data.

Facilitates the creation of intuitive figures to describe metabolomics data by utilizing Kyoto Encyclopedia of Genes and Genomes (KEGG) hierarchy data, and gathers functional orthology and gene data from the KEGG-REST API.

Connor Tiffany

A Metabolomics Analysis Tool for Intuitive Figures and
Convenient Metadata Collection

assign_hierarchy function

<dl><dt>count_data</dt>
<dd>a metabolomics count data frame with either a KEGG compound, orthology,
or a gene identifier column</dd>
<dt>keep_unknowns</dt>
<dd>a boolean of either TRUE or FALSE. TRUE keeps unannotated compounds,
FALSE removes them</dd>
<dt>identifier</dt>
<dd>a string that is either "KEGG" for metabolite, "KO" for orthology,
"Prokaryote" for organism, or "Eukaryote" for organism</dd></dl>

Arguments

Assign hierarchy metadata — assign_hierarchy

<dl>

<dt>count_data</dt>
<dd>a metabolomics count data frame with either a KEGG compound, orthology,
or a gene identifier column</dd>


<dt>keep_unknowns</dt>
<dd>a boolean of either TRUE or FALSE. TRUE keeps unannotated compounds,
FALSE removes them</dd>


<dt>identifier</dt>
<dd>a string that is either "KEGG" for metabolite, "KO" for orthology,
"Prokaryote" for organism, or "Eukaryote" for organism</dd>

</dl>

assign_hierarchy: Assign hierarchy metadata

Description

Usage

Arguments

Examples