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

## Documentation for package ‘omu’ version 1.1.0

- 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
check_zeros | Check data for zeros across samples within factor levels. Will determine if there are more zeros than a user specified threshold within any given factor level(s). Returns a vector of Metabolites that are 0 above the threshold in any given factor level.
count_fold_changes | Get counts for significant fold changes by metabolite class.
get_seqs | Get nucleotide and amino acid sequences for genes
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
omu_summary | omu_summary Performs comparison of means between two independent variables, 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 which parses flat text files
plate_omelette.genes | plate_omelette Internal method for KEGG_Gather which parses flat text files
plate_omelette.KO | plate_omelette Internal method for KEGG_Gather which parses flat text files
plate_omelette.rxn | plate_omelette Internal method for KEGG_Gather which parses flat text files
plate_omelette_rxnko | Clean up orthology metadata
plot_bar | Create a bar plot
plot_boxplot | Create a box plot
plot_heatmap | Create a heatmap
plot_rf_PCA | plot_rf_PCA
plot_variable_importance | plot_variable_importance
plot_volcano | Create a volcano plot
random_forest | random_forest Perform a classification or regression random forest model
ra_table | Creates a ratio table from the count_fold_changes function output.
read_metabo | Import a metabolomics count data frame
transform_metabolites | transform_metabolites
transform_samples | transform_samples