Network Centrality Metrics for Elastic-Net Regularized Models

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Documentation for package ‘glmSparseNet’ version 1.18.0

• 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