Man pages for sysbiomed/glmSparseNet
Network Centrality Metrics for Elastic-Net Regularized Models
| balancedCvFolds | Create balanced folds for cross validation using stratified... |
| buildLambda | Auxiliary function to generate suitable lambda parameters |
| buildStringNetwork | Build gene network from peptide ids |
| cv.glmSparseNet | Calculate cross validating GLM model with network-based... |
| degreeCor | Calculate the degree of the correlation network based on... |
| degreeCov | Calculate the degree of the covariance network based on xdata |
| dot-baseDir | Change base dir for '.runCache |
| dot-biomartLoad | Common call to biomaRt to avoid repetitive code |
| dot-buildFunctionDigest | Build digest of function from the actual code |
| dot-cacheCompression | Change cache.compression for run_cache |
| dot-calcPenalty | Calculate penalty based on data |
| dot-calculateResult | Calculate/load result and save if necessary |
| dot-combinedScore | Calculate combined score for STRINGdb interactions |
| dot-createDirectoryForCache | Create directories for cache |
| dot-curlWorkaround | Workaround for bug with curl when fetching specific ensembl... |
| dot-degreeGeneric | Generic function to calculate degree based on data |
| dot-digestCache | Default digest method |
| dot-glmSparseNetPrivate | Calculate GLM model with network-based regularization |
| dot-networkGenericParallel | Calculate the upper triu of the matrix |
| dot-networkWorker | Worker to calculate edge weight for each pair of ixI node and... |
| dot-runCache | Run function and save cache |
| dot-saveRunCache | Saving the cache |
| dot-showMessage | Show messages option in .runCache |
| dot-tempdirCache | Temporary directory for runCache |
| dot-writeReadme | Write a file in run-cache directory to explain the origin |
| downloadFileLocal | Download files to local temporary path |
| ensemblGeneNames | Retrieve ensembl gene names from biomaRt |
| geneNames | Retrieve gene names from biomaRt |
| glmSparseNet | Calculate GLM model with network-based regularization |
| glmSparseNet-package | glmSparseNet: Network Centrality Metrics for Elastic-Net... |
| hallmarks | Retrieve hallmarks of cancer count for genes |
| heuristicScale | Heuristic function to use in high dimensions |
| hubHeuristic | Heuristic function to penalize nodes with low degree |
| myColors | Custom pallete of colors |
| mySymbols | Custom pallete of symbols in plots |
| networkCorParallel | Calculates the correlation network |
| networkCovParallel | Calculates the covariance network |
| networkOptions | Setup network options |
| orphanHeuristic | Heuristic function to penalize nodes with high degree |
| protein2EnsemblGeneNames | Retrieve ensembl gene ids from proteins |
| separate2GroupsCox | Separate data in High and Low risk groups (based on Cox... |
| stringDBhomoSapiens | Download protein-protein interactions from STRING DB |
| string.network.700.cache | Cache of protein-protein network, as it takes some time to... |
