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The package is designed to take as input an m x n\nexpression matrix for some -omics modality (ie. metabolomics,\nlipidomics, proteomics, etc.) and jointly estimate the\nbiological network associations of each condition using the\nDNEA algorithm described in Ma et al. (2019). This approach\nprovides a framework for data-driven enrichment analysis across\ntwo experimental conditions that utilizes the underlying\ncorrelation structure of the data to determine feature-feature\ninteractions.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "output": "BiocStyle::html_document vignette: >\n%\\VignetteIndexEntry{Vignette Title}\n%\\VignetteEngine{knitr::rmarkdown} %\\VignetteEncoding{UTF-8}\n---", "Collate": "'JSEM-internals.R' 'aggregate-features.R' 'all-classes.R'\n'all-generics.R' 'all-methods.R' 'clustering-internals.R'\n'initiator.R' 'start-here.R' 'utilities-internals.R'\n'utilities-exported.R' 'primary.R'", "LazyData": "false", "URL": "https://github.com/Karnovsky-Lab/DNEA", "BugReports": "https://github.com/Karnovsky-Lab/DNEA/issues", "biocViews": "Metabolomics, Proteomics, Lipidomics,\nDifferentialExpression, NetworkEnrichment, Network, Clustering,\nDataImport", "Config/testthat/edition": 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"clusterNet", "title": "Identify metabolic modules within the biological networks using a consensus clustering approach", "topics": [ "clusterNet" ] }, { "page": "collapsed_DNEA-class", "title": "collapsed_DNEA", "topics": [ "collapsed_DNEA", "collapsed_DNEA-class" ] }, { "page": "consensusClusteringResults-class", "title": "consensusClusteringResults", "topics": [ "consensusClusteringResults", "consensusClusteringResults-class" ] }, { "page": "createDNEAobject", "title": "Initialize a DNEA object", "topics": [ "createDNEAobject" ] }, { "page": "datasetSummary-methods", "title": "Access the dataset_summary slot of a DNEA object", "topics": [ "datasetSummary", "datasetSummary,DNEA-method" ] }, { "page": "diagnostics-methods", "title": "Retrieve the diagnostic values for the input expression data", "topics": [ "diagnostics", "diagnostics,DNEA-method", "diagnostics,DNEAinputSummary-method" ] }, { "page": "DNEA-class", "title": "DNEA object", "topics": [ "DNEA-class", "show,DNEA-method" ] 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.csv files", "topics": [ "getNetworkFiles" ] }, { "page": "getNetworks", "title": "Construct the GLASSO-based biological Networks", "topics": [ "getNetworks" ] }, { "page": "includeMetadata", "title": "Add additional metadata to the DNEA object", "topics": [ "includeMetadata" ] }, { "page": "lambdas2Test-methods", "title": "Access the lambda values tested during hyper parameter optimization", "topics": [ "lambdas2Test", "lambdas2Test,DNEA-method" ] }, { "page": "massDataset2DNEA", "title": "Initialize a DNEA object from a mass_dataset object", "topics": [ "massDataset2DNEA" ] }, { "page": "metab_data", "title": "Feature meta data for the The Environmental Determinants of Diabetes in the Young (TEDDY) clinical trial", "topics": [ "metab_data" ] }, { "page": "metaData-methods", "title": "Retrieve metadata stored in a DNEA", "topics": [ "metaData", "metaData,DNEA-method" ] }, { "page": "netGSAresults-methods", "title": "Access the netGSA slot of a DNEA object", "topics": [ 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the lambda value used in analysis", "topics": [ "optimizedLambda", "optimizedLambda,DNEA-method", "optimizedLambda<-", "optimizedLambda<-,DNEA-method" ] }, { "page": "plotNetworks", "title": "Visualize the biological networks", "topics": [ "plotNetworks" ] }, { "page": "projectName-methods", "title": "Return the name of the current experiment", "topics": [ "projectName", "projectName,DNEA-method" ] }, { "page": "runNetGSA", "title": "Identify metabolic modules that are enriched across experimental conditions using NetGSA", "topics": [ "runNetGSA" ] }, { "page": "sampleNames-methods", "title": "Retrieve the sample names from the metadata slot.", "topics": [ "sampleNames", "sampleNames,DNEA-method" ] }, { "page": "selectionProbabilities-methods", "title": "Access and set the edge selection probabilities from stabilitySelection()", "topics": [ "selectionProbabilities", "selectionProbabilities,DNEA-method" ] }, { "page": "selectionResults-methods", "title": "Access and set the edge 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