Man pages for ncats/RaMP-DB
RaMP (Relational Database of Metabolomic Pathways)
| bhCorrect | Helper function to return a Benjamini-Hochberg (BH) corrected... |
| buildAnalyteOverlapPerRxnLevelUpsetDatafarme | Creates the input dataframe for the upset plot created in... |
| buildFrequencyTables | Return all analytes that map to unique pathways in a... |
| buildReactionClassesSunburstDatafarme | Creates the input dataframe for the sunburst plot created in... |
| checkIdPrefixes | Check for id prefixes By default, the function checks on... |
| chemicalClassEnrichment | Returns chemical class information comparing a metabolite... |
| chemicalClassSurvey | Returns chemical class information comparing a metabolite... |
| chemicalClassSurveyRampIdsConn | chemicalClassSurveyRampIdsConn2 is a helper function that... |
| chemicalClassSurveyRampIdsFullPopConn | chemicalClassSurveyRampIdsFullPopConn2 is a helper function... |
| cleanup | Generic function for removing RaMP identifiers and making... |
| combineStringLists | Utility method to combine two list to tally unique counts and... |
| compute_overlap_matrix | Compute overlaping matrix based on given list return by... |
| FilterFishersResults | Filter pathways by p-value cutoff for display and clustering |
| filterPathwaysByAnalyteCount | filterPathwaysByAnalyteCount utility method filtered a... |
| findAnalyteHasPathway | Find table of analyte has pathway from given pathway IDs... |
| findCluster | Perform fuzzy multiple linkage partitioning clustering on... |
| find_duplicate_pathways | Return list of duplicate Wikipathway IDs from Reactome. This... |
| findDuplicatePathways | Return list of duplicate Wikipathway IDs from Reactome. This... |
| getAnalyteFromPathway | Use fast search algorithm to find all pathways from given... |
| getChemicalProperties | Returns chemical properties given a metabolite list |
| getCurrentRaMPSourceDBVersions | Retrieve versions of each database within the current version... |
| getCurrentRaMPVersion | Retrieve RaMP version |
| getCustomPathwayFromAnalyte | Utility method supporting pathway analyses when file-based... |
| getEntityCountsFromSourceDBs | Retrieve counts of entitites (e.g. Metabolites, Pathways,... |
| getMetabChemClass | Returns chemical classes for classType |
| getMetabClassDataSources | Returns class data sources for metabolites |
| getMetabClassTypes | Returns class categories for metabolites |
| getMetaFromOnto | function that query database to find analytes in given... |
| 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... |
| getRaMPInfoFromAnalytes | Internal function for extracting annotations, used by pathway... |
| getRampSourceInfoFromAnalyteIDs | getRampSourceInfoFromAnalyteIDs Utility method to extract... |
| getReactionClassesForAnalytes | getReactionClassesForAnalytes returns reactions class and EC... |
| getReactionClassStats | Utility method that returns the number of rhea reaction count... |
| getReactionClassStatsOnAnalytes | Utility method that returns the number of rhea reaction count... |
| getReactionDetails | getReactionDetails returns general reaction information for a... |
| getReactionParticipants | getReactionParticipants returns protein information for a... |
| getReactionParticpantCounts | Utility method that evalutates the mapping counts for... |
| getReactionRheaURLs | Utility method that returns rhea reaction urls |
| getReactionsForAnalytes | getReactionsForAnalytes |
| getReactionsForRaMPCompoundIds | getReactionsForRaMPCompoundIds returns reactions for a... |
| getReactionsForRaMPGeneIds | getReactionsForRaMPGeneIds returns reactions for a collection... |
| getReactionsForSourceCompoundIds | getReactionsForSourceCompoundIds returns reactions for a... |
| getReactionsForSourceProteinIds | getReactionsForSourceProteinIds returns reactions for a... |
| getReactionSourceIdsFromReactionQuery | Utility method that returns the reaction source ids for a... |
| getRheaAnalyteReactionAssociations | getAnalyteReactionAssociations returns mets associated with... |
| getRheaEnzymesAndTransportersForMetabolites | getRheaEnzymesAndTransportersForMetabolites returns proteins... |
| getRheaMetabolitesForProteins | getRheaEnzymesAndTransportersForMetabolites returns proteins... |
| getTotalFoundInCategories | Utility method to return metabolite counts found in compound... |
| listAvailableRaMPDbVersions | Lists local and remotely available RaMP SQLite DB versions... |
| listToQueryString | listToQueryString utility method to convert an id list to a... |
| pathwayResultsPlot | Cluster and plot significant pathways by FDR-adjusted pval |
| plotAnalyteOverlapPerRxnLevel | Plots an interactive upset plot of overlapping input... |
| plotCataNetwork | Plots a network based on gene-metabolite relationships |
| plotReactionClasses | Plots an interactive sunburst plot of reaction class |
| processData | processData function generates pathway RampId frequency (gene... |
| queryReport | queryReport is a helper function to report on the number of... |
| RaMP | Connection to a RaMP database |
| rampFastCata | Retrieves analytes that involved in same reaction as input... |
| rampFastCataOriginal | Retrieves analytes that involved in same reaction as input... |
| rampFastPathFromSource | Fast search given a list of metabolites source Id |
| rampFindClassInfoFromSourceId | Get class info for an input of metabolite source Ids |
| rampFindSourceFromId | Find all source from given list of RaMP Ids |
| rampFindSourceRampId | Find rampId from given source ID The rampId can be plugged in... |
| rampFindSynonymFromSynonym | Find all synonym from a given metabolite's name This function... |
| removeLocalRampDB | Remove a RaMP database version from local file cache |
| runCombinedFisherTest | Do fisher test for only one pathway from search result... |
| runFisherTest | Do fisher test for only one pathway from search result... |
| runQuery | Get results from an SQL query to a RaMP database |
| segregateDataBySource | Separate input ids into lists based on database of origin |
| updateOverlapMatrices | Update and save the overlap matrices based on current version... |
| updateOverlapMatrix | Update the overlap matrix for store in the shiny app... |
| write_FishersResults | Function that writes Fishers Test results, after clustering... |
| writePathwaysToCSV | Function that writes output from getPathwayFromAnalyte() to a... |
