Man pages for zeynebkurtUCLA/Mergeomics
Integrative network analysis of omics data

job.kdaKey Driver Analyzing results
kda2cytoscapeGenerate input files for Cytoscape
kda2cytoscape.colorizeTrace module memberships of genes
kda2cytoscape.colormapAssign one color to each unique module
kda2cytoscape.driversSelect top key drivers for each module
kda2cytoscape.edgesFind edges of a given node with a specified depth
kda2cytoscape.execEvaluate each module separately for visualization
kda2cytoscape.identifyMatch identities with respect to given variable name
kda2himmeliGenerate input files for Himmeli
kda2himmeli.colorizeTrace module memberships of genes
kda2himmeli.colormapAssign one color to each unique module
kda2himmeli.driversSelect top key drivers for each module
kda2himmeli.edgesFind edges of a given node with a specified depth
kda2himmeli.execEvaluate each module separately for visualization
kda2himmeli.identifyMatch identities with respect to given variable name
kda.analyzeWeighted key driver analysis (wKDA) main function
kda.analyze.execAuxiliary function for weight key driver analysis (wKDA)
kda.analyze.simulateWeighted key driver analysis (wKDA) simulation
kda.analyze.testCalculate enrichment score for wKDA
kda.configureSet parameters for weighted key driver analysis (wKDA)
kda.finishOrganize and save results
kda.finish.estimateEstimate measures for accomplished wKDA results
kda.finish.saveSave full wKDA results
kda.finish.summarizeSummarize the wKDA results
kda.finish.trimTrim numbers before save
kda.preparePrepare graph topology for weighted key driver analysis
kda.prepare.overlapExtract overlapping co-hubs
kda.prepare.screenPrepare hubs and hubnets
kda.startImport data for weighted key driver analysis
kda.start.edgesImport nodes and edges of graph topology
kda.start.identifyConvert identities to indices for wKDA
kda.start.modulesImport module descriptions
Mergeomics-packageIntegrative network analysis of omics data
MSEA.KDA.onestepRun MSEA and/or KDA in one step
ssea2kdaGenerate inputs for wKDA
ssea2kda.analyzeApply second MSEA after merging the modules
ssea2kda.importImport genes and top markers from original files
ssea.analyzeMarker set enrichment analysis (MSEA)
ssea.analyze.observeCollect enrichment score statistics for MSEA
ssea.analyze.randgenesEstimate enrichment from randomized genes
ssea.analyze.randlociEstimate enrichment from randomized marker
ssea.analyze.simulateSimulate scores for MSEA
ssea.analyze.statisticMSEA statistics for enrichment score
ssea.controlAdd internal positive control modules for MSEA
ssea.finishOrganize and save MSEA results
ssea.finish.detailsOrganize and save module, gene, top locus, Ps of MSEA results
ssea.finish.fdrOrganize and save FDR results of the MSEA
ssea.finish.genesOrganize and save gene-realted MSEA results
ssea.metaMerge multiple MSEA results into meta MSEA
ssea.preparePrepare an indexed database for MSEA
ssea.prepare.countsCalculate hit counts up to a given quantile
ssea.prepare.structureConstruct hierarchical representation of components
ssea.startCreate a job for MSEA
ssea.start.configureCheck parameters before MSEA
ssea.start.identifyConvert identities to indices for MSEA
ssea.start.relabelUpdate gene symbols after merging overlapped markers
tool.aggregateAggregate the entries
tool.clusterHierarchical clustering of nodes
tool.cluster.staticStatic hierarchical clustering
tool.coalesceCalculate overlaps between groups (main function)
tool.coalesce.execFind, merge, and trim overlapping clusters
tool.coalesce.findFind overlapping clusters
tool.coalesce.mergeMerge overlapping clusters
tool.fdrEstimate False Discovery Rates (FDR)
tool.fdr.bhBenjamini and Hochberg False Discovery Rate
tool.fdr.empiricalEstimate Empirical False Discovery Rates
tool.graphConvert an edge list to a graph representation
tool.graph.degreeFind degrees of the nodes
tool.graph.listReturn edge list for each node
tool.metapEstimate meta P-values
tool.normalizeEstimate statistical scores based on Gauss distribution
tool.normalize.qualityCheck normalization quality
tool.overlapCalculate overlaps between groups of specified items
tool.readRead a data frame from a file
tool.saveSave a data frame in tab-delimited file
tool.subgraphDetermine network neighbors for a set of nodes
tool.subgraph.findFind edges to adjacent nodes
tool.subgraph.searchSearch neighborhoods for given nodes
tool.subgraph.statsCalculate node degrees and strengths
tool.translateTranslate gene symbols
tool.unifyConvert a distribution to uniform ranks
zeynebkurtUCLA/Mergeomics documentation built on May 14, 2019, 1:59 a.m.