# Network Centrality Metrics for Elastic-Net Regularized Models

## Documentation for package ‘glmSparseNet’ version 1.16.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

.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