# A Metabolomics Analysis Tool for Intuitive Figures and Convenient Metadata Collection

## Documentation for package ‘omu’ version 1.0.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

assign_hierarchy | Assign hierarchy metadata
c57_nos2KO_mouse_countDF | c57b6J nos2KO metabolomics count matrix
c57_nos2KO_mouse_metadata | c57b6J nos2KO meta data
count_fold_changes | Get counts for significant fold changes by metabolite class.
KEGG_gather | Gather metadata from KEGG for metabolites
KEGG_gather.cpd | Gather metadata from KEGG for metabolites
KEGG_gather.KO | Gather metadata from KEGG for metabolites
KEGG_gather.rxn | Gather metadata from KEGG for metabolites
make_omelette | Get metadata from KEGG API
omu_anova | Perform anova Performs an anova across all response variables. The function can take a maximum of 2 independent variables and perform an interaction term between them.
omu_summary | omu_summary Performs t test, standard deviation, standard error, FDR correction, fold change, log2FoldChange. The order effects the fold change values
PCA_plot | Create a PCA plot
pie_chart | Create a pie chart
plate_omelette | plate_omelette Internal method for KEGG_Gather
plate_omelette.genes | plate_omelette Internal method for KEGG_Gather
plate_omelette.rxn | plate_omelette Internal method for KEGG_Gather
plate_omelette_rxnko | Clean up orthology metadata
plot_bar | Create a bar plot
plot_volcano | Create a volcano plot
ra_table | Creates a ratio table from the count_fold_changes function output.
read_metabo | Import a metabolomics count data frame