Multi Omics Survival Clip

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Documentation for package ‘MOSClip’ version 1.3.3

• 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