Differential Network Enrichment Analysis for Biological Data

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Documentation for package ‘DNEA’ version 0.99.14

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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