Man pages for cavei/MOSClip
Multi Omics Survival Clip
| annotePathwayToFather | Convert pathways into a fathers |
| availableOmicMethods | Get available Omics Summarizing Methods |
| computeOmicsIntersections | Compute Omics Intersections |
| discreteClasses | From continous to discrete classes. |
| dummy_datasets | Function to create some fake dataset for testing purpose |
| evaluateResampling | Select stable pathway modules |
| extractBadPrognosisProfile | Extract the worst profile |
| extractRiskTable | Extrac the risk table from survminer object |
| extractSummaryFromBinary | Extract Summary Binary from MultiOmics Objects |
| extractSummaryFromCluster | Extract Summary CLuster from MultiOmics Objects |
| extractSummaryFromNumberOfEvents | Extract Summary Binary from MultiOmics Objects |
| extractSummaryFromPCA | Extract Summary PCA from MultiOmics Objects |
| guessInvolvement | Guess the most influent features from MultiOmics Survival... |
| guessInvolvementPathway | Guess the most influent features from MultiOmics Survival... |
| match_pathway_to_fathers | Remove pathways with no id in graphite |
| multiOmicsModuleInterAnalysis | Multi Omics Module Inter Module Analysis |
| MultiOmicsModules-class | Multi Omics Modules. |
| MultiOmicsPathway-class | Multi Omics Pathway. |
| multiOmicsSurvivalModuleTest | Compute Multi Omics Survival in Pathway Modules |
| multiOmicsSurvivalPathwayTest | Compute Multi Omics Survival in Pathways |
| multiPathwayModuleReport | Provide a data.frame of pathways module test results from... |
| multiPathwayReport | Summarize pathways' info from a list of MultiOmicsPathway... |
| Omics-class | Multi Omics Storage that extends '"list"' class. |
| plotGraphiteInCy | Plot graph in Cytoscape |
| plotModuleHeat | Plot heatmaps of the module by omics |
| plotModuleInGraph | Plot graph of the module by omics |
| plotModuleKM | Plot KM of the module by omics |
| plotModuleReport | Summarize and plot pathways' info from a MultiOmicsModule... |
| plotMultiPathwayReport | Summarize and plot pathways' info from a list of... |
| plotPathwayHeat | Plot heatmaps of the pathway by omics |
| plotPathwayKM | Plot KM of the pathway by omics |
| plotSurvivalBarcodes | Plot the patients barcodes |
| pvalueSummary | Compute pvalue Summary |
| resampling | Check if all the list object have the same order of pathway... |
| resamplingPathway | Resampling function for pathways |
| runSupertest | Performs statistical tests of the pathway intersections among... |
| showMOSpalette | Shows the MOSClip palette. |
| strip-functions | Strip feature type. |
| stripModulesFromPathways | Remove module number From Pathway Name |
| summarizeColumnsByMask | Multi Omics Module Inter Module Analysis |
| summarizeInCluster | Summarize Using Cluster Analysis |
| summarizeInClusterWithoutDictionary | Summarize Using Cluster Analysis with no dictionary to... |
| summarizeToBinaryDirectionalEvents | Summarize To Binary Directional Events |
| summarizeToBinaryEvents | Summarize To Binary Events |
| summarizeToNumberOfDirectionalEvents | Summarize With Directed Sum |
| summarizeToNumberOfEvents | Summarize To Number of Binary Events |
| summarizeWithPca | Summarize Using PCA |
