Man pages for califano-lab/MOMA
Multi Omic Master Regulator Analysis
| areaEnrich | aREA.enrich Compute aREA enrichment between all pairwise... |
| associateEvents | Use 'aREA' to calculate the enrichment between each genomic... |
| checkGeneMap | Check Gene Map |
| checkList | Check List of Assays |
| checkMAE | Check MultiAssayExperiment |
| checkPathways | Check Pathways |
| clusterRange | Cluster Range |
| clusterReliability | Cluster membership reliability estimated by enrichment... |
| cnvScoreStouffer | Integrate CNV scores |
| conditionalModel | Implements the conditional Bayes model to combine VIPER... |
| conditionalP | Get the conditional p-value of a gene |
| empiricalP | Get the empirical p-value from a distribution (vector) |
| example.gbm.mae | Glioblastoma (GBM) Example Dataset |
| fitCurvePercent | Fit based on fractional overall coverage of genomic events |
| gbm.pathways | Glioblastoma (GBM) Pathways |
| gene.map | Gene Location Mapping |
| genomicPlotSmall | Make small genomic plot |
| getCoverage | Get coverage of interactions |
| getDataFrame | Helper function to get data frame for bar plot plot.events... |
| getDiggitEmpiricalQvalues | Compute the empirical q-values of each genomic-event/VIPER... |
| getEmpiricalQvals | Get empirical qvals |
| getPvalsMatrix | Utility function |
| getSubtypeEventTables | Helper function to get subtype specific events |
| integrateFunction | Numerical integration of functions |
| integrateTZ | Integration with trapezoid method |
| makeCoverageDf | Helper function for making the coverage dataframe |
| makeSaturationPlots | Main function to generate the summary plots of the analysis |
| mapEntrez | Convert from entrez ids to hugo gene names |
| mapHugo | Convert from hugo gene names to entrez ids |
| mapScoresCnvBand | Map scores to cytoband location |
| mergeData | Helper function for mergeDataBySubtype |
| mergeDataBySubtype | Create data frame from coverage data, including number of... |
| mergeGenomicSaturation | mergeGenomicSaturation Create data frame from coverage data,... |
| mergeLists | Helper function |
| Moma-class | MOMA Object |
| momaConstructor | MOMA Constructor Function |
| mutSig | MutSig Blacklisted genes |
| oncoprintPlot | Function to plot genomic events in the style of... |
| pathwayDiggitIntersect | Combine DIGGIT inferences with pathway knowledge |
| plotEvents | Plot barchart of genomic events |
| rea | This function calculates an Enrichment Score of Association... |
| reaNULL | This function generates the NULL model function, which... |
| sampleNameFilter | Retain TCGA sample ids without the final letter designation... |
| sampleOverlap | The core function to compute which sample-specific... |
| sigInteractorsDIGGIT | Filter interactions from NES (DIGGIT) scores and... |
| sREA | Simple one-tail rank based enrichment analysis sREA (for... |
| stoufferIntegrate | dispatch method for either CNV location corrected or SNV |
| stoufferIntegrateDiggit | Use Stouffer's method to combine z-scores of DIGGIT... |
| subsetListInteractions | Helper function: subset a list to the set of keys supplied... |
| validDiggitInteractions | Return a set of events 'covered' by specified cMR-event... |
| viperGetSigTFS | Calculate p-values from pseudo zscores / VIPER aREA scores,... |
| viperGetTFScores | Function to normalize TF scores |
