Differential Network Enrichment Analysis for Biological Data


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Documentation for package ‘DNEA’ version 0.99.14

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