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 |