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

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...
getAnalyteFromPathwayUse fast search algorithm to find all pathways from given...
getMetaFromOntofunction that query database to find analytes in given...
getOntoFromMetaFunction that query database to find ontology information...
getPathwayFromAnalyteFunction that search analytes (gene or compounds) or a list...
loadOverlapMatricesLoad pathway overlap matrices for find_clusters function
plotCataNetworkPlots a network based on gene-metabolite relationships
rampFastCataRetrieves analytes that involved in same reaction as input...
rampFastPathFromSourceFast search given a list of metabolites source Id
rampFileOfAnalytes_tab4Generate dataframe from given files for shiny app input list...
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...
runRaMPappRun Shiny App
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 to a CSV file
writePathwaysToCSVFunction that writes output from getPathwayFromAnalyte() to a...
Mathelab/RaMP-DB documentation built on April 26, 2018, 2:40 a.m.