.baseDir                Change base dir for '.runCache
.biomartLoad            Common call to biomaRt to avoid repetitive code
.buildFunctionDigest    Build digest of function from the actual code
.cacheCompression       Change cache.compression for run_cache
.calcPenalty            Calculate penalty based on data
.calculateResult        Calculate/load result and save if necessary
.combinedScore          Calculate combined score for STRINGdb
                        interactions
.createDirectoryForCache
                        Create directories for cache
.curlWorkaround         Workaround for bug with curl when fetching
                        specific ensembl mirror
.degreeGeneric          Generic function to calculate degree based on
                        data
.digestCache            Default digest method
.networkGenericParallel
                        Calculate the upper triu of the matrix
.networkWorker          Worker to calculate edge weight for each pair
                        of ixI node and following
.runCache               Run function and save cache
.saveRunCache           Saving the cache
.showMessage            Show messages option in .runCache
.tempdirCache           Temporary directory for runCache
.writeReadme            Write a file in run-cache directory to explain
                        the origin
balancedCvFolds         Create balanced folds for cross validation
                        using stratified sampling
buildLambda             Auxiliary function to generate suitable lambda
                        parameters
buildStringNetwork      Build gene network from peptide ids
cv.glmDegree            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
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
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 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
