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<h1> Integrative network analysis of omics data
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</div><h2>Documentation for package ‘Mergeomics’ version 1.6.0</h2>
<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
<li><a href="../doc/index.html">User guides, package vignettes and other documentation.</a></li>
<li><a href="../NEWS">Package NEWS</a>.</li>
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<h2>Help Pages</h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="Mergeomics-package.html">Mergeomics-package</a></td>
<td>Integrative network analysis of omics data</td></tr>
<tr><td style="width: 25%;"><a href="job.kda.html">job.kda</a></td>
<td>Key Driver Analyzing results</td></tr>
<tr><td style="width: 25%;"><a href="kda.analyze.html">kda.analyze</a></td>
<td>Weighted key driver analysis (wKDA) main function</td></tr>
<tr><td style="width: 25%;"><a href="kda.analyze.exec.html">kda.analyze.exec</a></td>
<td>Auxiliary function for weight key driver analysis (wKDA)</td></tr>
<tr><td style="width: 25%;"><a href="kda.analyze.simulate.html">kda.analyze.simulate</a></td>
<td>Weighted key driver analysis (wKDA) simulation</td></tr>
<tr><td style="width: 25%;"><a href="kda.analyze.test.html">kda.analyze.test</a></td>
<td>Calculate enrichment score for wKDA</td></tr>
<tr><td style="width: 25%;"><a href="kda.configure.html">kda.configure</a></td>
<td>Set parameters for weighted key driver analysis (wKDA)</td></tr>
<tr><td style="width: 25%;"><a href="kda.finish.html">kda.finish</a></td>
<td>Organize and save results</td></tr>
<tr><td style="width: 25%;"><a href="kda.finish.estimate.html">kda.finish.estimate</a></td>
<td>Estimate measures for accomplished wKDA results</td></tr>
<tr><td style="width: 25%;"><a href="kda.finish.save.html">kda.finish.save</a></td>
<td>Save full wKDA results</td></tr>
<tr><td style="width: 25%;"><a href="kda.finish.summarize.html">kda.finish.summarize</a></td>
<td>Summarize the wKDA results</td></tr>
<tr><td style="width: 25%;"><a href="kda.finish.trim.html">kda.finish.trim</a></td>
<td>Trim numbers before save</td></tr>
<tr><td style="width: 25%;"><a href="kda.prepare.html">kda.prepare</a></td>
<td>Prepare graph topology for weighted key driver analysis</td></tr>
<tr><td style="width: 25%;"><a href="kda.prepare.overlap.html">kda.prepare.overlap</a></td>
<td>Extract overlapping co-hubs</td></tr>
<tr><td style="width: 25%;"><a href="kda.prepare.screen.html">kda.prepare.screen</a></td>
<td>Prepare hubs and hubnets</td></tr>
<tr><td style="width: 25%;"><a href="kda.start.html">kda.start</a></td>
<td>Import data for weighted key driver analysis</td></tr>
<tr><td style="width: 25%;"><a href="kda.start.edges.html">kda.start.edges</a></td>
<td>Import nodes and edges of graph topology</td></tr>
<tr><td style="width: 25%;"><a href="kda.start.identify.html">kda.start.identify</a></td>
<td>Convert identities to indices for wKDA</td></tr>
<tr><td style="width: 25%;"><a href="kda.start.modules.html">kda.start.modules</a></td>
<td>Import module descriptions</td></tr>
<tr><td style="width: 25%;"><a href="kda2cytoscape.html">kda2cytoscape</a></td>
<td>Generate input files for Cytoscape</td></tr>
<tr><td style="width: 25%;"><a href="kda2cytoscape.colorize.html">kda2cytoscape.colorize</a></td>
<td>Trace module memberships of genes</td></tr>
<tr><td style="width: 25%;"><a href="kda2cytoscape.colormap.html">kda2cytoscape.colormap</a></td>
<td>Assign one color to each unique module</td></tr>
<tr><td style="width: 25%;"><a href="kda2cytoscape.drivers.html">kda2cytoscape.drivers</a></td>
<td>Select top key drivers for each module</td></tr>
<tr><td style="width: 25%;"><a href="kda2cytoscape.edges.html">kda2cytoscape.edges</a></td>
<td>Find edges of a given node with a specified depth</td></tr>
<tr><td style="width: 25%;"><a href="kda2cytoscape.exec.html">kda2cytoscape.exec</a></td>
<td>Evaluate each module separately for visualization</td></tr>
<tr><td style="width: 25%;"><a href="kda2cytoscape.identify.html">kda2cytoscape.identify</a></td>
<td>Match identities with respect to given variable name</td></tr>
<tr><td style="width: 25%;"><a href="kda2himmeli.html">kda2himmeli</a></td>
<td>Generate input files for Himmeli</td></tr>
<tr><td style="width: 25%;"><a href="kda2himmeli.colorize.html">kda2himmeli.colorize</a></td>
<td>Trace module memberships of genes</td></tr>
<tr><td style="width: 25%;"><a href="kda2himmeli.colormap.html">kda2himmeli.colormap</a></td>
<td>Assign one color to each unique module</td></tr>
<tr><td style="width: 25%;"><a href="kda2himmeli.drivers.html">kda2himmeli.drivers</a></td>
<td>Select top key drivers for each module</td></tr>
<tr><td style="width: 25%;"><a href="kda2himmeli.edges.html">kda2himmeli.edges</a></td>
<td>Find edges of a given node with a specified depth</td></tr>
<tr><td style="width: 25%;"><a href="kda2himmeli.exec.html">kda2himmeli.exec</a></td>
<td>Evaluate each module separately for visualization</td></tr>
<tr><td style="width: 25%;"><a href="kda2himmeli.identify.html">kda2himmeli.identify</a></td>
<td>Match identities with respect to given variable name</td></tr>
<tr><td style="width: 25%;"><a href="Mergeomics-package.html">Mergeomics</a></td>
<td>Integrative network analysis of omics data</td></tr>
<tr><td style="width: 25%;"><a href="MSEA.KDA.onestep.html">MSEA.KDA.onestep</a></td>
<td>Run MSEA and/or KDA in one step</td></tr>
<tr><td style="width: 25%;"><a href="ssea.analyze.html">ssea.analyze</a></td>
<td>Marker set enrichment analysis (MSEA)</td></tr>
<tr><td style="width: 25%;"><a href="ssea.analyze.observe.html">ssea.analyze.observe</a></td>
<td>Collect enrichment score statistics for MSEA</td></tr>
<tr><td style="width: 25%;"><a href="ssea.analyze.randgenes.html">ssea.analyze.randgenes</a></td>
<td>Estimate enrichment from randomized genes</td></tr>
<tr><td style="width: 25%;"><a href="ssea.analyze.randloci.html">ssea.analyze.randloci</a></td>
<td>Estimate enrichment from randomized marker</td></tr>
<tr><td style="width: 25%;"><a href="ssea.analyze.simulate.html">ssea.analyze.simulate</a></td>
<td>Simulate scores for MSEA</td></tr>
<tr><td style="width: 25%;"><a href="ssea.analyze.statistic.html">ssea.analyze.statistic</a></td>
<td>MSEA statistics for enrichment score</td></tr>
<tr><td style="width: 25%;"><a href="ssea.control.html">ssea.control</a></td>
<td>Add internal positive control modules for MSEA</td></tr>
<tr><td style="width: 25%;"><a href="ssea.finish.html">ssea.finish</a></td>
<td>Organize and save MSEA results</td></tr>
<tr><td style="width: 25%;"><a href="ssea.finish.details.html">ssea.finish.details</a></td>
<td>Organize and save module, gene, top locus, Ps of MSEA results</td></tr>
<tr><td style="width: 25%;"><a href="ssea.finish.fdr.html">ssea.finish.fdr</a></td>
<td>Organize and save FDR results of the MSEA</td></tr>
<tr><td style="width: 25%;"><a href="ssea.finish.genes.html">ssea.finish.genes</a></td>
<td>Organize and save gene-realted MSEA results</td></tr>
<tr><td style="width: 25%;"><a href="ssea.meta.html">ssea.meta</a></td>
<td>Merge multiple MSEA results into meta MSEA</td></tr>
<tr><td style="width: 25%;"><a href="ssea.prepare.html">ssea.prepare</a></td>
<td>Prepare an indexed database for MSEA</td></tr>
<tr><td style="width: 25%;"><a href="ssea.prepare.counts.html">ssea.prepare.counts</a></td>
<td>Calculate hit counts up to a given quantile</td></tr>
<tr><td style="width: 25%;"><a href="ssea.prepare.structure.html">ssea.prepare.structure</a></td>
<td>Construct hierarchical representation of components</td></tr>
<tr><td style="width: 25%;"><a href="ssea.start.html">ssea.start</a></td>
<td>Create a job for MSEA</td></tr>
<tr><td style="width: 25%;"><a href="ssea.start.configure.html">ssea.start.configure</a></td>
<td>Check parameters before MSEA</td></tr>
<tr><td style="width: 25%;"><a href="ssea.start.identify.html">ssea.start.identify</a></td>
<td>Convert identities to indices for MSEA</td></tr>
<tr><td style="width: 25%;"><a href="ssea.start.relabel.html">ssea.start.relabel</a></td>
<td>Update gene symbols after merging overlapped markers</td></tr>
<tr><td style="width: 25%;"><a href="ssea2kda.html">ssea2kda</a></td>
<td>Generate inputs for wKDA</td></tr>
<tr><td style="width: 25%;"><a href="ssea2kda.analyze.html">ssea2kda.analyze</a></td>
<td>Apply second MSEA after merging the modules</td></tr>
<tr><td style="width: 25%;"><a href="ssea2kda.import.html">ssea2kda.import</a></td>
<td>Import genes and top markers from original files</td></tr>
<tr><td style="width: 25%;"><a href="tool.aggregate.html">tool.aggregate</a></td>
<td>Aggregate the entries</td></tr>
<tr><td style="width: 25%;"><a href="tool.cluster.html">tool.cluster</a></td>
<td>Hierarchical clustering of nodes</td></tr>
<tr><td style="width: 25%;"><a href="tool.cluster.static.html">tool.cluster.static</a></td>
<td>Static hierarchical clustering</td></tr>
<tr><td style="width: 25%;"><a href="tool.coalesce.html">tool.coalesce</a></td>
<td>Calculate overlaps between groups (main function)</td></tr>
<tr><td style="width: 25%;"><a href="tool.coalesce.exec.html">tool.coalesce.exec</a></td>
<td>Find, merge, and trim overlapping clusters</td></tr>
<tr><td style="width: 25%;"><a href="tool.coalesce.find.html">tool.coalesce.find</a></td>
<td>Find overlapping clusters</td></tr>
<tr><td style="width: 25%;"><a href="tool.coalesce.merge.html">tool.coalesce.merge</a></td>
<td>Merge overlapping clusters</td></tr>
<tr><td style="width: 25%;"><a href="tool.fdr.html">tool.fdr</a></td>
<td>Estimate False Discovery Rates (FDR)</td></tr>
<tr><td style="width: 25%;"><a href="tool.fdr.bh.html">tool.fdr.bh</a></td>
<td>Benjamini and Hochberg False Discovery Rate</td></tr>
<tr><td style="width: 25%;"><a href="tool.fdr.empirical.html">tool.fdr.empirical</a></td>
<td>Estimate Empirical False Discovery Rates</td></tr>
<tr><td style="width: 25%;"><a href="tool.graph.html">tool.graph</a></td>
<td>Convert an edge list to a graph representation</td></tr>
<tr><td style="width: 25%;"><a href="tool.graph.degree.html">tool.graph.degree</a></td>
<td>Find degrees of the nodes</td></tr>
<tr><td style="width: 25%;"><a href="tool.graph.list.html">tool.graph.list</a></td>
<td>Return edge list for each node</td></tr>
<tr><td style="width: 25%;"><a href="tool.metap.html">tool.metap</a></td>
<td>Estimate meta P-values</td></tr>
<tr><td style="width: 25%;"><a href="tool.normalize.html">tool.normalize</a></td>
<td>Estimate statistical scores based on Gauss distribution</td></tr>
<tr><td style="width: 25%;"><a href="tool.normalize.quality.html">tool.normalize.quality</a></td>
<td>Check normalization quality</td></tr>
<tr><td style="width: 25%;"><a href="tool.overlap.html">tool.overlap</a></td>
<td>Calculate overlaps between groups of specified items</td></tr>
<tr><td style="width: 25%;"><a href="tool.read.html">tool.read</a></td>
<td>Read a data frame from a file</td></tr>
<tr><td style="width: 25%;"><a href="tool.save.html">tool.save</a></td>
<td>Save a data frame in tab-delimited file</td></tr>
<tr><td style="width: 25%;"><a href="tool.subgraph.html">tool.subgraph</a></td>
<td>Determine network neighbors for a set of nodes</td></tr>
<tr><td style="width: 25%;"><a href="tool.subgraph.find.html">tool.subgraph.find</a></td>
<td>Find edges to adjacent nodes</td></tr>
<tr><td style="width: 25%;"><a href="tool.subgraph.search.html">tool.subgraph.search</a></td>
<td>Search neighborhoods for given nodes</td></tr>
<tr><td style="width: 25%;"><a href="tool.subgraph.stats.html">tool.subgraph.stats</a></td>
<td>Calculate node degrees and strengths</td></tr>
<tr><td style="width: 25%;"><a href="tool.translate.html">tool.translate</a></td>
<td>Translate gene symbols</td></tr>
<tr><td style="width: 25%;"><a href="tool.unify.html">tool.unify</a></td>
<td>Convert a distribution to uniform ranks</td></tr>
</table>
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