Network Centrality Metrics for Elastic-Net Regularized Models

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Documentation for package ‘glmSparseNet’ version 1.25.0

• 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