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| .calcPenalty | Calculate penalty based on data |
| .degreeGeneric | Generic function to calculate degree based on data |
| .glmSparseNetPrivate | Calculate GLM model with network-based regularization |
| .networkGenericParallel | Calculate the upper triu of the matrix |
| .networkWorker | Worker to calculate edge weight for each pair of ix.i node and following |
| biomart.load | Common call to biomaRt to avoid repetitive code |
| buildLambda | Auxiliary function to generate suitable lambda parameters |
| buildStringNetwork | Build gene network from peptide ids |
| calculate.combined.score | Calculate combined score for STRINGdb interactions |
| curl.workaround | Workaround for bug with curl when fetching specific ensembl mirror |
| cv.glmDegree | GLMNET cross-validation model penalizing nodes with small degree |
| cv.glmHub | GLMNET cross-validation model penalizing nodes with small degree |
| cv.glmOrphan | GLMNET cross-validation model penalizing nodes with high degree |
| cv.glmSparseNet | Calculate cross validating GLM model with network-based regularization |
| degreeCor | Calculate the degree of the correlation network based on xdata |
| degreeCov | Calculate the degree of the covariance network based on xdata |
| degreeSparsebn | Calculate degree of correlation matrix |
| downloadFileLocal | Download files to local temporary path |
| ensemblGeneNames | Retrieve ensembl gene names from biomaRt |
| geneNames | Retrieve gene names from biomaRt |
| glmDegree | GLMNET model penalizing nodes with small degree |
| glmHub | GLMNET model penalizing nodes with small degree |
| glmOrphan | GLMNET model penalizing nodes with high degree |
| glmSparseNet | Calculate GLM model with network-based regularization |
| 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 |
| 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 model) |
| string.network.700.cache | Cache of protein-protein network, as it takes some time to retrieve and process this will facilitate the vignette building |
| stringDBhomoSapiens | Download protein-protein interactions from STRING DB |