Mergeomics: Integrative network analysis of omics data

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The Mergeomics pipeline serves as a flexible framework for integrating multidimensional omics-disease associations, functional genomics, canonical pathways and gene-gene interaction networks to generate mechanistic hypotheses. It includes two main parts, 1) Marker set enrichment analysis (MSEA); 2) Weighted Key Driver Analysis (wKDA).

Author
Ville-Petteri Makinen, Le Shu, Yuqi Zhao, Zeyneb Kurt, Bin Zhang, Xia Yang
Date of publication
None
Maintainer
Zeyneb Kurt <zeyneb@ucla.edu>
License
GPL (>= 2)
Version
1.2.0

View on Bioconductor

Man pages

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

Files in this package

Mergeomics/DESCRIPTION
Mergeomics/NAMESPACE
Mergeomics/R
Mergeomics/R/cle.LS.R
Mergeomics/R/msea.kda.onestep.R
Mergeomics/build
Mergeomics/build/vignette.rds
Mergeomics/data
Mergeomics/data/job_kda_analyze.RData
Mergeomics/inst
Mergeomics/inst/NEWS
Mergeomics/inst/doc
Mergeomics/inst/doc/Mergeomics.R
Mergeomics/inst/doc/Mergeomics.Rnw
Mergeomics/inst/doc/Mergeomics.pdf
Mergeomics/inst/extdata
Mergeomics/inst/extdata/Significant_pathways.info.txt
Mergeomics/inst/extdata/Significant_pathways.txt
Mergeomics/inst/extdata/coexpr.info.txt
Mergeomics/inst/extdata/genes.hdlc_040kb_ld70.human_eliminated.txt
Mergeomics/inst/extdata/marker.hdlc_040kb_ld70.human_eliminated.txt
Mergeomics/inst/extdata/mergedModules.info.txt
Mergeomics/inst/extdata/mergedModules.txt
Mergeomics/inst/extdata/modules.mousecoexpr.liver.human.txt
Mergeomics/inst/extdata/msea2kda.nodes.txt
Mergeomics/inst/extdata/network.mouseliver.mouse.txt
Mergeomics/inst/extdata/symbols.txt
Mergeomics/inst/unitTests
Mergeomics/inst/unitTests/test_kda.analyze.R
Mergeomics/inst/unitTests/test_ssea.analyze.R
Mergeomics/man
Mergeomics/man/MSEA.KDA.onestep.Rd
Mergeomics/man/Mergeomics-package.Rd
Mergeomics/man/job.kda.Rd
Mergeomics/man/kda.analyze.Rd
Mergeomics/man/kda.analyze.exec.Rd
Mergeomics/man/kda.analyze.simulate.Rd
Mergeomics/man/kda.analyze.test.Rd
Mergeomics/man/kda.configure.Rd
Mergeomics/man/kda.finish.Rd
Mergeomics/man/kda.finish.estimate.Rd
Mergeomics/man/kda.finish.save.Rd
Mergeomics/man/kda.finish.summarize.Rd
Mergeomics/man/kda.finish.trim.Rd
Mergeomics/man/kda.prepare.Rd
Mergeomics/man/kda.prepare.overlap.Rd
Mergeomics/man/kda.prepare.screen.Rd
Mergeomics/man/kda.start.Rd
Mergeomics/man/kda.start.edges.Rd
Mergeomics/man/kda.start.identify.Rd
Mergeomics/man/kda.start.modules.Rd
Mergeomics/man/kda2cytoscape.Rd
Mergeomics/man/kda2cytoscape.colorize.Rd
Mergeomics/man/kda2cytoscape.colormap.Rd
Mergeomics/man/kda2cytoscape.drivers.Rd
Mergeomics/man/kda2cytoscape.edges.Rd
Mergeomics/man/kda2cytoscape.exec.Rd
Mergeomics/man/kda2cytoscape.identify.Rd
Mergeomics/man/kda2himmeli.Rd
Mergeomics/man/kda2himmeli.colorize.Rd
Mergeomics/man/kda2himmeli.colormap.Rd
Mergeomics/man/kda2himmeli.drivers.Rd
Mergeomics/man/kda2himmeli.edges.Rd
Mergeomics/man/kda2himmeli.exec.Rd
Mergeomics/man/kda2himmeli.identify.Rd
Mergeomics/man/ssea.analyze.Rd
Mergeomics/man/ssea.analyze.observe.Rd
Mergeomics/man/ssea.analyze.randgenes.Rd
Mergeomics/man/ssea.analyze.randloci.Rd
Mergeomics/man/ssea.analyze.simulate.Rd
Mergeomics/man/ssea.analyze.statistic.Rd
Mergeomics/man/ssea.control.Rd
Mergeomics/man/ssea.finish.Rd
Mergeomics/man/ssea.finish.details.Rd
Mergeomics/man/ssea.finish.fdr.Rd
Mergeomics/man/ssea.finish.genes.Rd
Mergeomics/man/ssea.meta.Rd
Mergeomics/man/ssea.prepare.Rd
Mergeomics/man/ssea.prepare.counts.Rd
Mergeomics/man/ssea.prepare.structure.Rd
Mergeomics/man/ssea.start.Rd
Mergeomics/man/ssea.start.configure.Rd
Mergeomics/man/ssea.start.identify.Rd
Mergeomics/man/ssea.start.relabel.Rd
Mergeomics/man/ssea2kda.Rd
Mergeomics/man/ssea2kda.analyze.Rd
Mergeomics/man/ssea2kda.import.Rd
Mergeomics/man/tool.aggregate.Rd
Mergeomics/man/tool.cluster.Rd
Mergeomics/man/tool.cluster.static.Rd
Mergeomics/man/tool.coalesce.Rd
Mergeomics/man/tool.coalesce.exec.Rd
Mergeomics/man/tool.coalesce.find.Rd
Mergeomics/man/tool.coalesce.merge.Rd
Mergeomics/man/tool.fdr.Rd
Mergeomics/man/tool.fdr.bh.Rd
Mergeomics/man/tool.fdr.empirical.Rd
Mergeomics/man/tool.graph.Rd
Mergeomics/man/tool.graph.degree.Rd
Mergeomics/man/tool.graph.list.Rd
Mergeomics/man/tool.metap.Rd
Mergeomics/man/tool.normalize.Rd
Mergeomics/man/tool.normalize.quality.Rd
Mergeomics/man/tool.overlap.Rd
Mergeomics/man/tool.read.Rd
Mergeomics/man/tool.save.Rd
Mergeomics/man/tool.subgraph.Rd
Mergeomics/man/tool.subgraph.find.Rd
Mergeomics/man/tool.subgraph.search.Rd
Mergeomics/man/tool.subgraph.stats.Rd
Mergeomics/man/tool.translate.Rd
Mergeomics/man/tool.unify.Rd
Mergeomics/tests
Mergeomics/tests/runTests.R
Mergeomics/vignettes
Mergeomics/vignettes/Mergeomics.Rnw
Mergeomics/vignettes/top5KDs.png