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 |