| Backpropagate | Run backpropagation for a single layer. In backpropagation, a... |
| BuildCoRegulationGraph | Construct a co-regulation graph where nodes are analytes, and... |
| BuildGraphDataFrame | Construct a data frame that includes all information needed... |
| CalculatePredictionCutoffs | Calculate minimum and maximum cutoffs for prediction. |
| CombineSubspaces | Combine subspaces (i.e. using Grassmann Manifold Technique -... |
| CombineSubspacesTest | Combine subspaces (i.e. using Grassmann Manifold Technique -... |
| CompositeModelSet-class | CompositeModelSet class |
| CompositePrediction | Obtain a prediction from a composite model, given the pairs... |
| ComputeAnalyteCoefMetafeature | Compute the importance using absolute value of analyte term... |
| ComputeClassificationError | Compute classification error. |
| ComputeCosineSimilarity | Compute cosine similarity between samples on an adjacency... |
| ComputeGlobalErrorMetafeature | Computes the importance as the median absolute error for all... |
| ComputeGlobalErrorMetafeatureTest | Computes the importance as the median absolute error for all... |
| computeGradient | Compute the gradient for a single layer neural network. |
| computeGradientForAveraging | Compute the gradient for a single layer neural network. |
| ComputeIndividualPerformance | Obtain a prediction from a composite model, given the pairs... |
| ComputeInteractionCoefMetafeature | Compute the importance using absolute value of interaction... |
| ComputeLocalErrorMetafeature | Computes the importance as the median absolute error for... |
| ComputeLocalErrorMetafeatureTest | Computes the importance as the median absolute error for... |
| ComputeMetaFeatureWeights | Compute the weight of each predictor given the weights of... |
| ComputePathwayMetafeature | Compute the importance using pathway membership. Predictor... |
| ComputePDFMetafeature | Computes the importance as the density in the probability... |
| ComputePvalMetafeature | Compute the importance using p-value of model interaction... |
| ComputeReactionMetafeature | Compute the importance using reaction membership. Predictor... |
| ComputeRMSE | Compute the normalized root mean squared error. |
| ComputeSignificance | Compute the significance value for a given prediction. You... |
| ComputeTScore | Compute t-score for a prediction using the paired t-test. The... |
| CosineSimilarityToTrainingOnSingleDataType | Compute cosine similarity between a testing sample and each... |
| CosineSimilarityToTrainingOnSubspace | Compute cosine similarity between a testing sample and each... |
| DerivativeOfActivation | Compute the derivative of the error by the predictor. |
| Dhat | Compute the D-hat value, which is the denominator value of... |
| DhatPrime | Compute the D-hat value, which is the derivative of the... |
| DoModelSetup | This function performs the following tasks: 1. Run IntLIM to... |
| DoModelSetupFromIntLim | This function performs the following tasks: (IntLIM models of... |
| DoPrediction | Predict Y given current weights. |
| DoSignificancePropagation | Obtain a prediction from a composite model, given the pairs... |
| DoSingleTrainingIteration | Train the graph learning model, using the specifications in... |
| DoTestSetupAndPrediction | Sets up the test data so that it is in the correct format,... |
| DoTestSetupOnly | Sets up the test data so that it is in the correct format,... |
| DoUnweightedTestSetupAndPrediction | Predict the test values using the learned model. |
| FindOptimalSubspaceClustering | Finds the optimal subspace clustering (i.e. using Grassmann... |
| FormatInput | Format the input for graph-based learning. This input... |
| GetGlobalErrorCorr | Creates a Spearman correlation matrix of the prediction... |
| GetMetaFeatures | Computes the metafeatures for each sample and model. |
| GetPredictorIDs | Function for obtaining database identifiers for each... |
| GetTestMetaFeatures | Computes the metafeatures for each sample and model in the... |
| InitializeGraphLearningModel | Find edges that share nodes and add them to a data frame. |
| Model-class | Model class |
| ModelInput-class | ModelInput class |
| ModelResults-class | ModelResults class |
| Nhat | Compute the N-hat value, which is the numerator value of the... |
| NhatPrime | Compute the N-hat value, which is the derivative of the... |
| ObtainCompositeModels | Obtain the list of pairs in a composite model. Do this by... |
| ObtainSubgraphNeighborhoods | Obtain the list of pairs in a composite model. |
| ObtainUnweightedModel | Obtain the combination of predictors without including any... |
| OneHotEncoding | Perform one-hot encoding of the sample metadata. This is... |
| OptimizeMetaFeatureCombo | Optimize the combination of predictors by metafeatures alone... |
| Predict | Run a prediction on new data using the graph learning model. |
| ProjectPredictionsOntoGraph | Given a graph and a phenotype prediction for each significant... |
| PruneBackwardStepwise | Given multiple composite predictors, prune the predictors... |
| PruneExhaustive | Given multiple composite predictors, evaluate each... |
| PruneForwardStepwise | Given multiple composite predictors, prune the predictors... |
| PrunePredictors | Given multiple composite predictors, prune the predictors... |
| PruneStepwiseParallel | Given multiple composite predictors, prune the predictors... |
| RunPairwisePrediction | Given each significant pairwise model and the input data,... |
| SplitTrainingAndTesting | Splits input data into training and testing sets given a... |
