A Metabolomics Analysis Tool for Intuitive Figures and
Convenient Metadata Collection
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Documentation for package ‘omu’ version 1.1.2
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 |