MOSClip                 MOSClip: Multi-Omics Survival Clip
MultiOmicsModules-class
                        Multi Omics Modules.
MultiOmicsPathway-class
                        Multi Omics Pathway.
Omics-class             Omics.
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
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
getPathFathers          Retrieves pathways relatives
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
minOrNA                 Minimum or NA
multiOmics              Omics class object with TCGA ovarian data
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)
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
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
runSupertest            Performs a Exact test - analysis of omics
                        intersection
selectStablePathwaysModules
                        Select stable pathway modules
showMOSpalette          Shows the MOSClip palette.
showModule              A generic function showing pathway's module
                        info
showOmics               A generic functions showing parameter
                        associated with each omics
showPathway             A generic function showing pathway info
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
