Man pages for borenstein-lab/mimosa2
Model-based Integration of Metabolite Observations and Species Abundances
| add_metadata_to_metabolite_summary | Do basic enrichment testing of between-group metabolite... |
| add_residuals | Returns a melted data table of species and their scaled cmps... |
| add_rev_rxns | Add reverse of reversible reactions to edge list network |
| add_to_network | Add reactions to a network. Will set stoichiometry and copy... |
| agora_kegg_mets | Finds KEGG IDs for a list of AGORA metabolites |
| basic_correlation_matrix | Basic species-metaoblite correlation for comparison |
| blast_seqs | BLASTS a set of sequences against a database |
| build_generic_network | Function called by run_pipeline to get species-specific... |
| build_metabolic_model | Build species-specific metabolic model for MIMOSA2 analysis |
| build_species_networks_w_agora | Taxa mapping functions, MIMOSA2 June 2018 Finds close AGORA... |
| calculate_var_shares | Wrapper function to calculate contributions to variance,... |
| calculate_var_shares_linear | Calculates contributions to variance from a contribution... |
| check_config_table | Check configuration table formatting |
| check_ref_data | Check that MIMOSA2 can access reference databases in the... |
| cmp_met_plot | Plot CMP values vs metabolite concentrations for a single... |
| cmp_species_contributions | Evaluate species contributors for a single metabolite with... |
| cmp_species_contributions_picrust | Evaluate species contributors for a single metabolite with... |
| compare_met | Compare a single set each of CMP scores and metabolite... |
| contribs_by_species_list | Get a list of relevant gene abundances for each species and... |
| correct | #' Title #' #' @param nrow #' @param ncol #' #' @return #'... |
| download_reference_data | Uses the provided OTU table to generate a contribution table... |
| download_ribosomal_ref_seqs | Uses the provided OTU table to generate a contribution table... |
| emm_to_edge_list | Convert stoichiometric matrix to edge list of reactions |
| filter_currency_metabolites | Remove metabolites linked to many reactions from a metabolic... |
| filter_species_abunds | Filter species found in few samples and/or low abundance |
| fit_cmp_mods | Fits model scaling total CMPs to metabolite concentrations |
| fit_cmp_net_edit | Greedy algorithm to test network improvements /refine rxn... |
| fit_single_scaling_mod | Fits single model scaling total CMPs to concentrations of a... |
| gene_contributions | Identify potential important gene contributors for each... |
| generate_contribution_table_using_picrust | Uses the provided OTU table to generate a contribution table... |
| generate_genomic_network | Create a community metabolic network model using a few... |
| generate_network_template_kegg | Generate community metabolic network template from the KEGG... |
| generate_preprocessed_networks | Generate preprocessed reference databases for MIMOSA2 |
| get_all_consistent_metabolite_info | Read output of runMimosa.R from files to make a table of all... |
| get_all_singleSpec_cmps | Get single-species CMP scores for every OTU and metabolite |
| get_analysis_summary | Calculate general summary statistics on the results of a... |
| get_cmp_scores | Calculate CMP scores based on community network and gene... |
| get_cmp_scores_kos | Updated version of getting all sample-level CMP scores from a... |
| get_cmp_summary | Get summary of CMP score basis across all samples |
| get_compound_format | Determines whether a list of compounds is in KEGG or AGORA... |
| get_genomic_content_from_picrust_table | Returns the column from the picrust tables that corresponds... |
| get_kegg_network | Imports pre-generated KEGG network models for each species |
| get_kegg_reaction_info | Get basic KEGG reaction and KO info in a unified format |
| getModelInfo | Reads metabolic model in Cobra/Matlab format |
| get_net_dist | Get network distances between 2 compounds |
| get_non_rev_rxns | Get non-reverible reactions of network. |
| get_rep_seqs_from_otus | Returns representative 16S sequences for a set of... |
| get_S_mats | Convert stoichiometric matrix to edge list of reactions |
| get_spec_contribs | Perform a series of steps related to identifying... |
| get_species_cmp_scores | Updated version of getting all single-species CMP scores for... |
| get_subset_picrust_ko_table | Returns the melted picrust ko table corresponding to the... |
| get_summary_stats | Calculate basic statistics summarizing MIMOSA results |
| get_text | Get text constants used for MIMOSA interactive app from... |
| getWScores | Get Wilcoxon scores for Jaeckel's dispersion calculations |
| g_legend | Get legend from a ggplot2 object |
| humann2_format_contributions | Function for reformatting a Humann2 stratified KO abundance... |
| img_uri | Generate img URIs for putting plots in output table |
| j.disp.fit | Jaeckel's dispersion from model predictions |
| j.disp.mean | Jaeckel's dispersion from the mean (null) |
| j.disp.rsq.adj | Adjusted R-squared for a rank-based model |
| kegg_agora_mets | Finds AGORA IDs for a list of KEGG metabolites (i.e. when... |
| kos_from_species | Function for getting ko abundances from species abundance... |
| load_agora_models | Reads a set of AGORA models from Matlab files |
| make_contrib_network | Convert edge list and node list to class network object for... |
| make_gene_species_contributor_table | Make table of species-specific gene and reaction contributors... |
| make_metabolite_species_contribution_table | Make table summarizing species contributions for each... |
| make_network_matrix | Convert edge list network format to matrix format, including... |
| make_pairwise_met_matrix | Make a data vector into a pairwise difference matrix (can be... |
| make_perm_mat | Make matrix of permutations for mantel test with a row for... |
| make_unnormalized_single_spec | Get functional relative abundances from a single species'... |
| mantel_2sided | Modification of vegan mantel test to test 2-sided or... |
| map_seqvar | Assign seq vars to OTUs or AGORA models using vsearch |
| map_to_kegg_webchem | #' Convert metabolite name table to KEGG metabolite table #'... |
| met_names | Get metabolite name for KEGG ID(s) |
| met_table_fix | Set column name to compound and filter metabolites with too... |
| otus_to_db | Returns AGORA species that a list of Greengenes OTUs were... |
| plot_all_cmp_mets | Generate a list of plots of CMP values vs metabolite... |
| plot_contrib_net | Use ggnetwork to make a network visualization of metabolite... |
| plot_contributions | Plot species contributions for a single metabolite |
| plot_metabolite_concentrations | Make heatmap plot of metabolite concentrations across samples... |
| plot_metabolite_counts | Make bar plot of MIMOSA outcome counts in different... |
| plot_summary_contributions | Plot summary of metabolite-species contributions |
| print_taxa_contributor_table | Return summarized and concise data on taxonomic contributors... |
| process_gene_contribs | Process table of gene and reaction contributors |
| process_mat_met_file | Returns the column from the picrust tables that corresponds... |
| process_metabolite_summary | Add summary columns to metabolite 'node' file of MIMOSA... |
| randomize_net | Randomize a metabolic network edge list by randomly sampling... |
| randomString | Get random string (for saving temp files) |
| rank_based_rsq_contribs | Calculates contributions to variance for Rfit regression... |
| read_files | Read in processed files and assign keys to datasets. Sets NA... |
| read_mimosa2_files | Read in files for a MIMOSA 2 analysis |
| refine_rev_rxns | Convert metabolite name table to KEGG metabolite table |
| run_all_metabolites | Runall function to do complete predictions and comparison for... |
| run_all_metabolites2 | Runall function to do complete predictions and evaluate... |
| run_all_metabolites_FBA2 | Run full MIMOSA1 analysis on simulation data (2019) |
| run_mimosa1 | Run full MIMOSA1 analysis (2019) |
| run_mimosa2 | Run a MIMOSA 2 analysis |
| run_samp_shapley_analysis | Calculates contributions to variance using permutation/subset... |
| run_shapley_contrib_analysis | Calculates contributions to variance using permutation/subset... |
| run_shuffle | Run one iteration of MIMOSA analysis with a randomized... |
| single_gene_cmp | Calculate scores based on only a single gene. |
| single_spec_musicc | Get contributors for every metabolite and save |
| spec_table_fix | Set column name of OTU table to "OTU", and remove taxa with... |
| sum_to_genus | Sum OTU data to the genus level |
| taxonomic_contributor_heatmap_plot_grid | Make plot of individual metabolites and their taxonomic... |
| test_m2_analysis | Run toy analysis to test package installation |
| test_met_enrichment | Test for enrichment of list of known microbial metabolites in... |
| transform_cmps | Apply a transformation to CMP data |
| transform_mets | Apply a transformation to metabolite data |
| var_shares_cmps | Get variance share contributions to CMP scores for all... |
