Man pages for Mathelab/RaMP-DB
RaMP (Relational Database of Metabolomic Pathways)
| compute_overlap_matrix | Compute overlaping matrix based on given list return by... |
| connectToRaMP | Connect to RaMP database (requires mysql password when... |
| FilterFishersResults | Filter pathways by p-value cutoff for display and clustering |
| findAnalyteHasPathway | Find table of analyte has pathway from given pathway IDs... |
| findCluster | Perform fuzzy multiple linkage partitioning clustering on... |
| getAnalyteFromPathway | Use fast search algorithm to find all pathways from given... |
| getMetaFromOnto | function that query database to find analytes in given... |
| getOntoFromMeta | Function that query database to find ontology information... |
| getPathwayFromAnalyte | Function that search analytes (gene or compounds) or a list... |
| plotCataNetwork | Plots a network based on gene-metabolite relationships |
| processData | processData function generates pathway RampId frequency (gene... |
| rampFastCata | Retrieves analytes that involved in same reaction as input... |
| rampFastPathFromSource | Fast search given a list of metabolites source Id |
| rampFileOfAnalytes_tab4 | Generate dataframe from given files for shiny app input list... |
| 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... |
| runCombinedFisherTest | Do fisher test for only one pathway from search result... |
| runFisherTest | Do fisher test for only one pathway from search result... |
| runRaMPapp | Run Shiny App |
| sysdataObject | sysdataObject() generates sysdata.rda object from exdata dir... |
| 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 to a CSV file |
| writePathwaysToCSV | Function that writes output from getPathwayFromAnalyte() to a... |
