# Network Centrality Metrics for Elastic-Net Regularized Models

## Documentation for package ‘glmSparseNet’ version 1.22.0

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

## Help Pages

.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
.runCache-method | 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
balanced.cv.folds | Create balanced folds for cross validation using stratified sampling
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
cv.glmHub | Calculate cross validating GLM model with network-based regularization
cv.glmOrphan | Calculate cross validating GLM model with network-based regularization
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
downloadFileLocal | Download files to local temporary path
ensemblGeneNames | Retrieve ensembl gene names from biomaRt
geneNames | Retrieve gene names from biomaRt
glmDegree | Calculate GLM model with network-based regularization
glmHub | Calculate GLM model with network-based regularization
glmOrphan | Calculate GLM model with network-based regularization
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
my.colors | Custom pallete of colors
my.symbols | Custom pallete of symbols in plots
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