.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
balanced.cv.folds       Create balanced folds for cross validation
base.dir                change base.dir for run.cache
biomart.load            Common call to biomaRt to avoid repetitive code
build.function.digest   Build digest of function from the actual code
buildLambda             Auxiliary function to generate suitable lambda
                        parameters
buildStringNetwork      Build gene network from peptide ids
cache.compression       change cache.compression for run.cache
calculate.combined.score
                        Calculate combined score for STRINGdb
                        interactions
calculate.result        Calculate/load result and save if necessary
create.directory.for.cache
                        Create directories for cache
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
digest.cache            Default digest method
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
glmSparseNet.options    Constants for 'glmSparseNet' package
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
my.colors               Custom pallete of colors
my.symbols              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
run.cache               Run function and save cache
run.cache,function-method
                        Run function and save cache
save.run.cache          Saving the cache
separate2GroupsCox      Separate data in High and Low risk groups
                        (based on Cox model)
show.message            Show messages option in run.cache
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
tempdir.cache           Temporary directory for runCache
write.readme            Write a file in run-cache directory to explain
                        the origin
