Man pages for Sage-Bionetworks/metanetwork
Network meta analysis
| applySparrowBonferroni | Applies Bonferroni Correction to a Sparrow Network Object |
| applySparrowFDR | Applies FDR Correction to a Sparrow Network Object |
| aracne | This function applies ARACNE on the data |
| arbitrarySparsity | This function Builds an arbitary sparse network |
| buildConsensus | This function builds the Consensus Network from the component... |
| c3netWrapper | This function wraps c3net implementation |
| calcHyperPval | Compute Hypergeometric PValue |
| computeBICcurve | This Function Computes a Network BIC Curve |
| computeDriverDistance | Compute Graph Distance |
| computeDriverDistancePvalue | Compute Driver Distance P-Value |
| compute.LocalModularity | Find Local Modularity (NQ) |
| compute.Modularity | Find Global Modularity (Q) |
| compute.ModularityDensity | Find Global Modularity (Qds) |
| compute.ModuleQualityMetric | Find Modularity Quality |
| correlation | Compute a Correlation Matrix |
| covarianceSelection | Covariance Selection with Graphical Lasso |
| covarianceSelectionBisection | Covariance Selection with Bisection Optimization |
| covarianceSelectionMBPath | Covariance based on Neighborhood Selection |
| covarianceSelectionPath | Covariance Selection with Path BIC Selection |
| deployNetworkSparsity | This function deploys arbitary sparsity on a list of networks |
| fastlm | Fast Linear Modeling |
| fastlmbic | Fast Linear Modeling BIC |
| fdrThres | FDR Threshold |
| findModules.CFinder | Find Modules with CFinder |
| findModules.CFinder.once | This function tries to get modules from network adjacency... |
| findModules.consensusCluster | Finds Consensus Clusters |
| findModules.consensusKmeans | Finds Moduless With Kmeans Clustering |
| findModules.edge_betweenness | Find Modules with Network Adjacency |
| findModules.edge_betweenness.once | Find Modules with Network Adjacency Single iteration |
| findModules.fast_greedy | Find Modules with iGraph Fast and Greedy algorithm |
| findModules.fast_greedy.once | Find Modules Fast and Greedy |
| findModules.GANXiS | Find Modules with GANXiS |
| findModules.GANXiS.once | Find Modules using GANXIS |
| findModules.hclust | Find Modules with Hierarchical Clustering |
| findModules.infomap | Find Modules using graph adjacency |
| findModules.infomap.once | Find Modules using graph adjacency |
| findModules.label_prop | Wraps Finding Modules with Graph Adjacency |
| findModules.label_prop.once | Find Modules with Graph Adjacency |
| findModules.leading_eigen | Find Modules with Leading Eigen Edges |
| findModules.leading_eigen.once | Find Modules with Leading Eigen Edges |
| findModules.linkcommunities | Find Modules with Network Adjacency Matrix Using Link... |
| findModules.linkcommunities.once | Find Modules with Network Adjacency Matrix Using Link... |
| findModules.louvain | Find Modules with Network Adjacency Matrix Using Louvain... |
| findModules.louvain.once | Find Modules with Network Adjacency Matrix Using Louvain... |
| findModules.megena | Find Modules with Megena Clustering |
| findModules.spinglass | Find Modules with Network Adjacency Matrix Using Spinglass... |
| findModules.spinglass.once | Find Modules with Network Adjacency Matrix Using spinglass... |
| findModules.walktrap | Find Modules with Network Adjacency Matrix Using Walktrap... |
| findModules.walktrap.once | Find Modules with Network Adjacency Matrix Using Walktrap... |
| fisherEnrichment | Fishers Enrichment Analysis |
| genie3 | Run genie3 |
| installAracne | This function applies ARACNE on the data |
| lassoAIC | Grab AIC Solution for Lasso |
| lassoBIC | Grab BIC Solution for Lasso |
| lassoCV1se | Grab CV1se Solution for Lasso Regression |
| lassoCVmin | Grab CV1min Solution for Lasso Regression |
| metaNet-package | metaNet: Statistical network exploration toolkit |
| mpiWrapper | Runs Sparrow Regression |
| mrnetWrapper | Implements mrnet |
| multiplot | Multiple plot function |
| rankConsensus | Ranks Consensus networks |
| rankConsensus2 | Ranks Consensus networks with ties. |
| rankedEdgeList | Rank edges of a coexpression matrix |
| regulatorAnalysis.directed | Function to Identify Network Regulators from Directed... |
| regulatorAnalysis.directed_weighted | Function to Identify Network Regulators from Directed... |
| regulatorAnalysis.undirected | Function to Identify Network Regulators from Undirected... |
| regulatorAnalysis.undirected_weighted | Function to Identify Network Regulators from Undirected... |
| ridgeAIC | Grab AIC Solution for Ridge Regression |
| ridgeBIC | Grab BIC Solution for Ridge Regression |
| ridgeCV1se | Grab CV1se Solution for Ridge Regression |
| ridgeCVmin | Grab CV1min Solution for Ridge Regression |
| run.consensus.cluster | Runs Consensus Clustering Algorithm |
| score.nodes | Scores Nodes From Regulator Discovery |
| simulateNetworkData | Simulate Network Data |
| sparrow2Z | Runs vbsr with a 2Z cutoff for a gene across a matrix |
| sparrowNetwork | Runs wraps vbsr across a matrix |
| sparrowZ | Runs vbsr gene across a matrix |
| synGetFiles | This function pulls files from a synapse project |
| tigress | Runs tigress on an expression matrix |
| wgcnaSoftThreshold | Runs WGCNA |
| wgcnaTOM | Runs WGCNA TOMsimilarity |
| winsorizeData | Winsorize a Gene Expression Matrix |
