BICscores               Access the BIC scores for each lambda value
                        evaluated
BICtune                 Optimize the lambda regularization parameter
                        for the glasso-based network models using
                        Bayesian-information Criterion
CCsummary               Retrieves the summary results of consensus
                        clustering
DNEA-class              DNEA object
DNEA-package            DNEA: Differential Network Enrichment Analysis
                        for Biological Data
DNEAinputSummary-class
                        DNEAinputSummary
T1Dmeta                 Sample meta data for the The Environmental
                        Determinants of Diabetes in the Young (TEDDY)
                        clinical trial
TEDDY                   Example expresion data set from The
                        Environmental Determinants of Diabetes in the
                        Young (TEDDY) clinical trial
addExpressionData       Include custom normalized data in the DNEA
                        object
adjacencyGraph          Retrieve the adjacency graph for the case,
                        control, or joint network
adjacencyMatrix         Retrieve the weighted or unweighted adjacency
                        matrix
aggregateFeatures       Aggregate correlated features into a single
                        feature class
clusterNet              Identify metabolic modules within the
                        biological networks using a consensus
                        clustering approach
collapsed_DNEA-class    collapsed_DNEA
consensusClusteringResults-class
                        consensusClusteringResults
createDNEAobject        Initialize a DNEA object
datasetSummary          Access the dataset_summary slot of a DNEA
                        object
diagnostics             Retrieve the diagnostic values for the input
                        expression data
dnw                     Example results for DNEA
edgeList                Access the edge list
expressionData          Access expression data within a DNEA object,
featureNames            Retrieve the feature names from the metadata
                        slot.
filterNetworks          Filter the adjacency matrices to only the edges
                        that meet the filter conditions
getNetworkFiles         Save network information to .csv files
getNetworks             Construct the GLASSO-based biological Networks
includeMetadata         Add additional metadata to the DNEA object
lambdas2Test            Access the lambda values tested during hyper
                        parameter optimization
massDataset2DNEA        Initialize a DNEA object from a mass_dataset
                        object
metaData                Retrieve metadata stored in a DNEA
metab_data              Feature meta data for the The Environmental
                        Determinants of Diabetes in the Young (TEDDY)
                        clinical trial
netGSAresults           Access the netGSA slot of a DNEA object
networkGroupIDs         Access and set the experimental group labels
networkGroups           Retrieve the unique group values of the
                        experimental condition
nodeList                Access the node list
numFeatures             Retrieve the total number of features in the
                        dataset
numSamples              Retrieves the total number of samples in the
                        dataset
optimizedLambda         Access the lambda value used in analysis
plotNetworks            Visualize the biological networks
projectName             Return the name of the current experiment
runNetGSA               Identify metabolic modules that are enriched
                        across experimental conditions using NetGSA
sampleNames             Retrieve the sample names from the metadata
                        slot.
selectionProbabilities
                        Access and set the edge selection probabilities
                        from stabilitySelection()
selectionResults        Access and set the edge selection results from
                        stabilitySelection()
stabilitySelection      Stability selection calculates selection
                        probabilities for every possible
                        feature-feature interaction within the input
                        data
subnetworkMembership    Retrieve the subnetwork membership for each
                        feature
sumExp2DNEA             Initialize a DNEA from SummarizedExperiment
