# Multi Omics Survival Clip

## Documentation for package ‘MOSClip’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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