assign_hierarchy: Assign hierarchy metadata

In omu: A Metabolomics Analysis Tool for Intuitive Figures and Convenient Metadata Collection

Assign hierarchy metadata

Description

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

Usage

assign_hierarchy(count_data, keep_unknowns, identifier)

Arguments

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

Examples

assign_hierarchy(count_data = c57_nos2KO_mouse_countDF, keep_unknowns = TRUE, identifier = "KEGG")

omu documentation built on Oct. 17, 2023, 1:06 a.m.