Man pages for ncats/RaMP-DB
RaMP (Relational Database of Metabolomic Pathways)
| createRaMPInput | Produce RaMP input from metabolite metadata data.frame object... |
| filterEnrichResults | Filter enrichment results by p-value cutoff for display and... |
| findCluster | Perform fuzzy multiple linkage partitioning clustering on... |
| getAnalyteFromPathway | Use fast search algorithm to find all pathways from given... |
| getChemClass | Returns chemical class information comparing a metabolite... |
| getChemicalProperties | Returns chemical properties given a metabolite list |
| getCurrentRaMPSourceDBVersions | Retrieve versions of each database within the current version... |
| getCurrentRaMPVersion | Retrieve RaMP version |
| getEntityCountsFromSourceDBs | Retrieve counts of entitites (e.g. Metabolites, Pathways,... |
| getMetabChemClass | Returns chemical classes for classType |
| getMetabClassTypes | Returns class categories for metabolites |
| getMetaFromOnto | function that query database to find mets in given ontologies |
| getOntoFromMeta | Function that query database to find ontology information... |
| getOntologies | Returns list of available ontologies from database |
| getPathwayFromAnalyte | Function that search analytes (gene or compounds) or a list... |
| getPathwayNameList | Retrieve list of pathway names |
| getPrefixesFromAnalytes | Query to retrieve database ID prefixes for analyte types |
| getRaMPAnalyteIntersections | Retrieve RaMP Analyte Source Intersections, these indicate... |
| getReactionClassesForAnalytes | getReactionClassesForAnalytes returns reactions class and EC... |
| getReactionDetails | getReactionDetails returns general reaction information for a... |
| getReactionParticipants | getReactionParticipants returns protein information for a... |
| getReactionsForAnalytes | getReactionsForAnalytes returns all associated reactions for... |
| get_remote_db_version_list | List RaMP db versions |
| getRheaAnalyteReactionAssociations | getAnalyteReactionAssociations returns mets associated with... |
| listAvailableRaMPDbVersions | Lists local and remotely available RaMP SQLite DB versions... |
| package-deprecated | deprecated functions - to be removed in RaMP 4.0 |
| plotAnalyteOverlapPerRxnLevel | Plots an interactive upset plot of overlapping input... |
| plotCataNetwork | Plots a network based on gene-metabolite relationships |
| plotChemicalClass | Plots an interactive sunburst plot of chemical classes |
| plotOntologyEnrichmentResults | Cluster and plot significant ontologies by FDR-adjusted pVal |
| plotPathwayResults | Cluster and plot significant pathways by FDR-adjusted pVal |
| plotReactionClasses | Plots an interactive sunburst plot of reaction class |
| RaMP | Connection to a RaMP database |
| rampFastCata | Retrieves analytes that involved in same reaction as input... |
| removeLocalRampDB | Remove a RaMP database version from local file cache |
| runEnrichChemClass | Returns chemical class information comparing a metabolite... |
| runEnrichOntologies | Enrichment analysis for metabolite ontology mappings |
| runEnrichPathways | Do fisher test for only one pathway from search result... |
| runEnrichReactionClass | Enrichment analysis for analyte-reaction class mappings |
| runQuery | Get results from an SQL query to a RaMP database |
| writeFishersResults | Function that writes Fishers Test results, after clustering... |
| writePathwaysToCSV | Function that writes output from getPathwayFromAnalyte() to a... |
