.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
buildLambda             Auxiliary function to generate suitable lambda
                        parameters
buildStringNetwork      Build gene network from peptide ids
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
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
