Man pages for sysbiomed/glmSparseNet
Network Centrality Metrics for Elastic-Net Regularized Models

balancedCvFoldsCreate balanced folds for cross validation using stratified...
buildLambdaAuxiliary function to generate suitable lambda parameters
buildStringNetworkBuild gene network from peptide ids
cv.glmSparseNetCalculate cross validating GLM model with network-based...
degreeCorCalculate the degree of the correlation network based on...
degreeCovCalculate the degree of the covariance network based on xdata
dot-baseDirChange base dir for '.runCache
dot-biomartLoadCommon call to biomaRt to avoid repetitive code
dot-buildFunctionDigestBuild digest of function from the actual code
dot-cacheCompressionChange cache.compression for run_cache
dot-calcPenaltyCalculate penalty based on data
dot-calculateResultCalculate/load result and save if necessary
dot-combinedScoreCalculate combined score for STRINGdb interactions
dot-createDirectoryForCacheCreate directories for cache
dot-curlWorkaroundWorkaround for bug with curl when fetching specific ensembl...
dot-degreeGenericGeneric function to calculate degree based on data
dot-digestCacheDefault digest method
dot-glmSparseNetPrivateCalculate GLM model with network-based regularization
dot-networkGenericParallelCalculate the upper triu of the matrix
dot-networkWorkerWorker to calculate edge weight for each pair of ixI node and...
dot-runCacheRun function and save cache
dot-saveRunCacheSaving the cache
dot-showMessageShow messages option in .runCache
dot-tempdirCacheTemporary directory for runCache
dot-writeReadmeWrite a file in run-cache directory to explain the origin
downloadFileLocalDownload files to local temporary path
ensemblGeneNamesRetrieve ensembl gene names from biomaRt
geneNamesRetrieve gene names from biomaRt
glmSparseNetCalculate GLM model with network-based regularization
glmSparseNet-packageglmSparseNet: Network Centrality Metrics for Elastic-Net...
hallmarksRetrieve hallmarks of cancer count for genes
heuristicScaleHeuristic function to use in high dimensions
hubHeuristicHeuristic function to penalize nodes with low degree
myColorsCustom pallete of colors
mySymbolsCustom pallete of symbols in plots
networkCorParallelCalculates the correlation network
networkCovParallelCalculates the covariance network
networkOptionsSetup network options
orphanHeuristicHeuristic function to penalize nodes with high degree
protein2EnsemblGeneNamesRetrieve ensembl gene ids from proteins
separate2GroupsCoxSeparate data in High and Low risk groups (based on Cox...
stringDBhomoSapiensDownload protein-protein interactions from STRING DB
string.network.700.cacheCache of protein-protein network, as it takes some time to...
sysbiomed/glmSparseNet documentation built on Feb. 17, 2024, 1:38 p.m.