Man pages for biodev/packageDir
Tool for in silico functional analysis design and exploration of relation between genomic function and aberration.
| abDrugOverlapAnalysis | abDrugOverlapAnalysis |
| addBangForBuck | addBangForBuck |
| addCohortToIndividuals | Adds path enrichment information from cohort to paths found... |
| addCorrections | Function to add corrections to the corrections file.... |
| addPathwayImagesWithSelection | Add network diagrams of affected pathways. |
| addSequenceCaptureArm | Add sequence capture data input arm. |
| allInteractiveMainFunction | Run pathMod in interactive mode. |
| armDescriptionList | Get all arm descriptions |
| autoRunFromSettings | Automatically run set of analyses from a set of loaded... |
| BangForBuck | Get pathway overlaps. |
| checkFileCopyDefault | checkFileCopyDefault |
| compareSources | Allows comparrison of summary statistics for all loaded... |
| coreOverlapAnalysis | The central function used in an overlap analysis |
| correctByHgncHelper | Correct gene symbols using the HGNChelper package |
| corsym | Correct unofficial gene symbols. |
| DataArm-class | DataArm |
| DataSummary | Display summaries of loaded data. |
| dot-loadGraphitePaths | load graphite-supplied pathways |
| downloadHugoLookupTable | Obtain full HUGO gene symbol look up table. |
| extractPathNames | Get names of significant pathways. |
| getAlternateNames | getAlternateNames |
| getBasicSettings | Get settings object pre-loaded for example analysis |
| getComments | getComments() |
| getDefaultPaths | Retreive the default set of cellular pathways. |
| getDefaultSettings | getDefaultSettings |
| getGenesFromPaths | Get gene identifiers from a list of pathways. |
| getHugoSymbols | getHugoSymbols |
| getHumanPathIds | Pull out human path ids from the reactome.db annotation... |
| getLoadedPathSummaryRunner | Get 'path_summary_runner' object. |
| getNodePositionTable | Get position of nodes in cytoscape diagram. . |
| getPathIdsToTarget | getPathIdsToTarget |
| getPaths | Get set of cellular pathways |
| getPathsWithGenes | Get the names of the pathways containing submitted genes. |
| getPathwaysRecords | getPathwaysRecords |
| getPublicationRefs | getPublicationRefs() |
| getReactomeBiopax | Download biopax files for reactome pathways. |
| getReactomeIds | Get reactome database ids, give reactome path ids. |
| getStudyObject | getStudyObject |
| getTestPathSummaryRunner | Returns an example of the PathSummaryRunner reference class... |
| getTestPGM | Get an example patient gene matrix |
| getTestStudyObject | Get a Study object containing moc data. |
| getTestStudySettings | Get settings for the three basic study arms: functional,... |
| hypergeometricPathEnrichment | hypergeometric Path Enrichment analysis function for... |
| importAllGraphite | Import all pathway repositories from the graphite package to... |
| initiateStudy | initiateStudy |
| list_to_table | Convert list of vectors to bipartate graph format. |
| loadBasicArms | Load the basic set of analysis arms for use in a study |
| loadDataArm | loadDataArm |
| loadPathSigTests | loadPathSigTests |
| loadStudy | Loads a study from a file name. |
| makeDrugSelectionWorksheet | Uses genomic data from the provided Study object to produce a... |
| nodeNamesFromLabels | nodeNamesFromLabels |
| openPGM | openPGM |
| Path_Detail-class | Path_Detail class |
| PathSummaryRunner-class | PathSummaryRunner |
| patientSummaryToNozzleReport | Make a Nozzle report from an individual patient's results |
| PolyPhenFromMaf | orchestrates creation of polyphen input file from .maf file |
| prepPathListForSave | prepPathListForSave() |
| printProgramState | printProgramState |
| runArm | runArm |
| runDrugWorksheet | Run the drug selection worksheet. |
| runSomaticMutationsProcessing | Main execution function for entry of somatic mutation data,... |
| saveDataWorkUpNotes | saveDataWorkUpNotes |
| saveStudy | saveStudy |
| SaveToHTML | Save results to an HTML page. |
| selectAndLoadSettings | Load settings from a file folder tree into a Study object. |
| setBorderColors | setBorderColors |
| setCutoff | Set the cutoff for drug screen score |
| setNodeColors | setNodeColors() |
| settingList | settingList |
| Study-class | Study |
| StudyMetaData-class | StudyMetaData |
| summarize_by | summarize_by |
| summaryTable | Main pathway analysis function. |
| twoHistOnePlot | Puts two histograms on the same plot. |
| unfactorize | Replace factors/levels in a data.frame and use plain strings... |
| whichPaths | whichPaths |
