.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-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 |