Man pages for MOMA
Multi Omic Master Regulator Analysis

areaEnrichaREA.enrich Compute aREA enrichment between all pairwise...
associateEventsUse 'aREA' to calculate the enrichment between each genomic...
checkGeneMapCheck Gene Map
checkListCheck List of Assays
checkMAECheck MultiAssayExperiment
checkPathwaysCheck Pathways
clusterRangeCluster Range
clusterReliabilityCluster membership reliability estimated by enrichment...
cnvScoreStoufferIntegrate CNV scores
conditionalModelImplements the conditional Bayes model to combine VIPER...
conditionalPGet the conditional p-value of a gene
empiricalPGet the empirical p-value from a distribution (vector)
example.gbm.maeGlioblastoma (GBM) Example Dataset
fitCurvePercentFit based on fractional overall coverage of genomic events
gbm.pathwaysGlioblastoma (GBM) Pathways
gene.mapGene Location Mapping
genomicPlotSmallMake small genomic plot
getCoverageGet coverage of interactions
getDataFrameHelper function to get data frame for bar plot plot.events...
getDiggitEmpiricalQvaluesCompute the empirical q-values of each genomic-event/VIPER...
getEmpiricalQvalsGet empirical qvals
getPvalsMatrixUtility function
getSubtypeEventTablesHelper function to get subtype specific events
integrateFunctionNumerical integration of functions
integrateTZIntegration with trapezoid method
makeCoverageDfHelper function for making the coverage dataframe
makeSaturationPlotsMain function to generate the summary plots of the analysis
mapEntrezConvert from entrez ids to hugo gene names
mapHugoConvert from hugo gene names to entrez ids
mapScoresCnvBandMap scores to cytoband location
mergeDataHelper function for mergeDataBySubtype
mergeDataBySubtypeCreate data frame from coverage data, including number of...
mergeGenomicSaturationmergeGenomicSaturation Create data frame from coverage data,...
mergeListsHelper function
Moma-classMOMA Object
momaConstructorMOMA Constructor Function
mutSigMutSig Blacklisted genes
oncoprintPlotFunction to plot genomic events in the style of...
pathwayDiggitIntersectCombine DIGGIT inferences with pathway knowledge
plotEventsPlot barchart of genomic events
reaThis function calculates an Enrichment Score of Association...
reaNULLThis function generates the NULL model function, which...
sampleNameFilterRetain TCGA sample ids without the final letter designation...
sampleOverlapThe core function to compute which sample-specific...
sigInteractorsDIGGITFilter interactions from NES (DIGGIT) scores and...
sREASimple one-tail rank based enrichment analysis sREA (for...
stoufferIntegratedispatch method for either CNV location corrected or SNV
stoufferIntegrateDiggitUse Stouffer's method to combine z-scores of DIGGIT...
subsetListInteractionsHelper function: subset a list to the set of keys supplied...
validDiggitInteractionsReturn a set of events 'covered' by specified cMR-event...
viperGetSigTFSCalculate p-values from pseudo zscores / VIPER aREA scores,...
viperGetTFScoresFunction to normalize TF scores
MOMA documentation built on Nov. 8, 2020, 6:01 p.m.