Man pages for ncats/RaMP-DB
RaMP (Relational Database of Metabolomic Pathways)

bhCorrectHelper function to return a Benjamini-Hochberg (BH) corrected...
buildFrequencyTablesReturn all analytes that map to unique pathways in a...
checkIdPrefixesCheck for id prefixes By default, the function checks on...
chemicalClassEnrichmentReturns chemical class information comparing a metabolite...
chemicalClassSurveyReturns chemical class information comparing a metabolite...
chemicalClassSurveyRampIdsConnchemicalClassSurveyRampIdsConn is a helper function that...
chemicalClassSurveyRampIdsFullPopConnchemicalClassSurveyRampIdsFullPopConn is a helper function...
cleanupGeneric function for removing RaMP identifiers and making...
compute_overlap_matrixCompute overlaping matrix based on given list return by...
connectToRaMPConnect to RaMP database (requires mysql password when...
FilterFishersResultsFilter pathways by p-value cutoff for display and clustering
findAnalyteHasPathwayFind table of analyte has pathway from given pathway IDs...
findClusterPerform fuzzy multiple linkage partitioning clustering on...
find_duplicate_pathwaysReturn list of duplicate Wikipathway IDs from Reactome. This...
getAnalyteFromPathwayUse fast search algorithm to find all pathways from given...
getChemicalPropertiesReturns chemical properties given a metabolite list
getCurrentRaMPSourceDBVersionsRetrieve versions of each database within the current version...
getCurrentRaMPVersionRetrieve RaMP version
getEntityCountsFromSourceDBsRetrieve counts of entitites (e.g. Metabolites, Pathways,...
getMetabChemClassReturns chemical classes for classType
getMetabClassDataSourcesReturns class data sources for metabolites
getMetabClassTypesReturns class categories for metabolites
getMetaFromOntofunction that query database to find analytes in given...
getOntoFromMetaFunction that query database to find ontology information...
getOntologiesReturns list of available ontologies from database
getPathwayFromAnalyteFunction that search analytes (gene or compounds) or a list...
getPathwayNameListRetrieve list of pathway names
getPrefixesFromAnalytesQuery to retrieve database ID prefixes for analyte types
getRaMPAnalyteIntersectionsRetrieve RaMP Analyte Source Intersections, these indicate...
getRaMPInfoFromAnalytesInternal function for extracting annotations, used by pathway...
getTotalFoundInCategoriesUtility method to return metabolite counts found in compound...
pathwayResultsPlotCluster and plot significant pathways by FDR-adjusted pval
plotCataNetworkPlots a network based on gene-metabolite relationships
processDataprocessData function generates pathway RampId frequency (gene...
queryReportqueryReport is a helper function to report on the number of...
rampFastCataRetrieves analytes that involved in same reaction as input...
rampFastCataOriginalRetrieves analytes that involved in same reaction as input...
rampFastPathFromSourceFast search given a list of metabolites source Id
rampFindClassInfoFromSourceIdGet class info for an input of metabolite source Ids
rampFindSourceFromIdFind all source from given list of RaMP Ids
rampFindSourceRampIdFind rampId from given source ID The rampId can be plugged in...
rampFindSynonymFromSynonymFind all synonym from a given metabolite's name This function...
runCombinedFisherTestDo fisher test for only one pathway from search result...
runFisherTestDo fisher test for only one pathway from search result...
segregateDataBySourceSeparate input ids into lists based on database of origin
setConnectionToRaMPSet Connection Parameters or RaMP
updateOverlapMatricesUpdate and save the overlap matrices based on current version...
updateOverlapMatrixUpdate the overlap matrix for store in the shiny app...
write_FishersResultsFunction that writes Fishers Test results, after clustering...
writePathwaysToCSVFunction that writes output from getPathwayFromAnalyte() to a...
ncats/RaMP-DB documentation built on Sept. 26, 2022, 4:37 a.m.