| MOSClip-package | MOSClip: Multi-Omics Survival Clip |
| addResamplingCounts | Select stable pathway modules |
| annotePathwayToFather | Find Pathway Fathers |
| availableOmicMethods | Get available Omics Summarizing Methods |
| checkOrder | Check if all the list object have the same order of pathway module |
| compPCs | Regular PCA |
| computeFreqs | Compute Frequencies in a Named List |
| computeOmicsIntersections | Compute Omics Intersections |
| computePCs | compute PCs. |
| convertPathway | A generic function to convert pathway |
| coxrsummary | Cox Robust Model Analysis |
| createCoxObj | Create Cox Object |
| createDataModule | Create Data Module |
| createMOMView | Create the list of covariates that are going to be tested |
| downloadPathwayRelationFromReactome | Download Reactome Pathway Relations |
| estimateExprCov | Estimate Single Covariance Matrix |
| extractCliquesFromDag | Extract the maximal cliques |
| 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 |
| filterExpr | Check if all the list object have the same order of pathway module |
| filterMultiOmicsForSamples | Check if all the list object have the same order of pathway module |
| getPathFathers | Retrieves pathways relatives |
| getPathwaysModulesSuccess | Select stable pathway modules |
| glmTest | Two-classes glm test. |
| guessInvolvement | Guess the most influent features from MultiOmics Survival or Two-class results. |
| guessInvolvementPathway | Guess the most influent features from MultiOmics Survival or Two-class results. |
| id2name | Convert id to pathway name |
| makeOmics | Omics class initializer function |
| makePositiveDefinite | Make positive and definite covariance matrix |
| mapPathwaysIDfromGraphite | Map Pathways ID from Graphite |
| mergeCol | Check if all the list object have the same order of pathway module |
| minOrNA | Minimum or NA |
| mmmoralize | Extract the maximal cliques |
| MOSClip | MOSClip: Multi-Omics Survival Clip |
| multiOmics | Omics class object with TCGA ovarian data |
| 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 |
| multiOmicsTopo | Omics class object with TCGA ovarian data for topological analysis |
| multiOmicsTwoClassModuleTest | Computes Multi Omics Two-Class in Pathway Modules |
| multiOmicsTwoClassPathwayTest | Compute Multi Omics Two-Class in Pathways |
| multiPathwayModuleReport | Provides a Table of the Modules Test Results |
| multiPathwayReport | Summarize pathways' info from a list of MultiOmicsPathway objects (MOP) |
| Omics | Omics. |
| Omics-class | Omics. |
| ovarianDataset | ExperimentList class object with TCGA ovarian data |
| plotFrequencies | Plot Frequencies of Pathway Fathers for Omics intersection |
| plotModuleHeat | Plot a Heatmap of a Module by Omics |
| plotModuleInGraph | Plot a Directed Graph of the MultiOmicsModules Object |
| plotModuleKM | Plot Kaplan-Meier survival curves of a specific module |
| plotModuleReport | Plot a table of a 'MultiOmicsModules' (MOM) object |
| plotMultiPathwayReport | Summarize and plot pathways' info from a list of 'MultiOmicsPathway' (MOP) |
| plotPathwayHeat | Plot heatmaps of the pathway by omics |
| plotPathwayKM | Plot Kaplan-Meier survival curves of a specific pathway |
| preparePerms | Check if all the list object have the same order of pathway module |
| pvalueSummary | Compute pvalue Summary |
| reactSmall | PathwayList of pathways from Reactome |
| removeSelfLoops | Remove self loops from a graphNEL |
| resamplingModulesSurvival | Resampling function for survival analysis on modules |
| resamplingModulesTwoClass | Resampling function for two-class analysis on modules |
| resamplingPathwaySurvival | Resampling function for survival analysis on modules |
| resamplingPathwayTwoClass | Resampling function for two-class analysis on modules |
| resolveAndOrder | Check if all the list object have the same order of pathway module |
| runSupertest | Performs a Exact test - analysis of omics intersection |
| selectStablePathwaysModules | Select stable pathway modules |
| showModule | A generic function showing pathway's module info |
| showModule-method | Multi Omics Modules. |
| showMOSpalette | Shows the MOSClip palette. |
| showOmics | A generic functions showing parameter associated with each omics |
| showOmics-method | Omics. |
| showPathway | A generic function showing pathway info |
| showPathway-method | Multi Omics Pathway. |
| sparseCompPCs | Sparse PCA |
| stripModulesFromPathways | Remove Module Number From Pathway Name |
| summarizeInCluster | Summarize Using Cluster Analysis |
| summarizeOmicsResByMinPvalue | Summarize Omics Covaraites By Min Pvalue |
| 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 |
| survivalcox | Cox Model Analysis |
| survivalcoxr | Cox Robust Model Analysis |
| topoCompPCs | Topological PCA |