Man pages for tbradley1013/KEGGerator
Identify genomic functionality with KEGG
| as_keggerator | Convert an object into class keggerator |
| filter_orgs | Filter OTUs and kegg organisms |
| genomic_func_heatmap | Genomic Functional Heatmap |
| get_datasets | Get Updated KEGG datasets |
| get_enzyme_modules | Query all modules related to each enzyme in a dataset |
| get_enzymes | Query all enzymes related to each genome in the dataset |
| get_org_ids | retrieve KEGG genome id for all organims |
| get_orthologies | Query all orthologies related to each genome in the dataset |
| get_orthology_modules | Query all modules related to each orthology in a dataset |
| get_pathway_enzymes | Query all enzymes associated with a given pathway |
| get_pathway_modules | Query all modules associated with a given pathway |
| get_pathway_orthologies | Query all orthologies associated with a given pathway |
| has_complete_function | returns genomes that have all the functions in specified... |
| has_specific_function | find all genomes that complete all of the desired functions |
| is_kegg_tbl | Check whether KEGGerator datasets have the correct class |
| keggerator | A keggerator object |
| keggerator_uncertainty | Calculate total uncertainty |
| keggtap | Create a keggtap object |
| orgs_tibble | extract organisms from tax table or tax tibble |
| otu_ref | Create a otu reference table |
| otu_tibble | Convert OTU table to tibble |
| reexports | Objects exported from other packages |
| sam_tibble | Convert sam_data to tibble |
| tax_tibble | Convert tax table to tibble |
