Package: glmSparseNet 1.23.0

André Veríssimo

glmSparseNet: Network Centrality Metrics for Elastic-Net Regularized Models

glmSparseNet is an R-package that generalizes sparse regression models when the features (e.g. genes) have a graph structure (e.g. protein-protein interactions), by including network-based regularizers. glmSparseNet uses the glmnet R-package, by including centrality measures of the network as penalty weights in the regularization. The current version implements regularization based on node degree, i.e. the strength and/or number of its associated edges, either by promoting hubs in the solution or orphan genes in the solution. All the glmnet distribution families are supported, namely "gaussian", "poisson", "binomial", "multinomial", "cox", and "mgaussian".

Authors:André Veríssimo [aut, cre], Susana Vinga [aut], Eunice Carrasquinha [ctb], Marta Lopes [ctb]

glmSparseNet_1.23.0.tar.gz
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glmSparseNet.pdf |glmSparseNet.html✨
glmSparseNet/json (API)
NEWS

# Install 'glmSparseNet' in R:
install.packages('glmSparseNet', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/sysbiomed/glmsparsenet/issues

Datasets:
  • string.network.700.cache - Cache of protein-protein network, as it takes some time to retrieve and process this will facilitate the vignette building

On BioConductor:glmSparseNet-1.23.0(bioc 3.20)glmSparseNet-1.22.0(bioc 3.19)

bioconductor-package

29 exports 1.08 score 167 dependencies 1 mentions

Last updated 2 months agofrom:63a16f5ca4

Exports:balancedCvFoldsbuildLambdabuildStringNetworkcv.glmDegreecv.glmHubcv.glmOrphancv.glmSparseNetdegreeCordegreeCovensemblGeneNamesgeneNamesglmDegreeglmHubglmOrphanglmSparseNethallmarksheuristicScalehubHeuristicmy.colorsmy.symbolsmyColorsmySymbolsnetworkCorParallelnetworkCovParallelnetworkOptionsorphanHeuristicprotein2EnsemblGeneNamesseparate2GroupsCoxstringDBhomoSapiens

Dependencies:abindAnnotationDbiaskpassbackportsBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobbootbroomcachemcarcarDatacheckmateclicliprcodetoolscolorspacecommonmarkcorrplotcowplotcpp11crayoncurldata.tableDBIdbplyrDelayedArraydigestdplyrevaluateexactRankTestsfansifarverfastmapfilelockforcatsforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicDataCommonsGenomicFeaturesGenomicRangesggplot2ggpubrggrepelggsciggsignifggtextglmnetgluegridExtragridtextgtablehighrhmshttrhttr2IRangesisobanditeratorsjpegjsonliteKEGGRESTkm.ciKMsurvknitrlabelinglambda.rlatticelifecyclelme4magrittrmarkdownMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmaxstatmemoisemgcvmimeminqaMultiAssayExperimentmunsellmvtnormnlmenloptrnnetnumDerivopensslpbkrtestpillarpkgconfigplogrpngpolynomprettyunitsprogresspurrrquantregR6RaggedExperimentrappdirsRColorBrewerRcppRcppEigenRCurlreadrrestfulrRhtslibrjsonrlangRsamtoolsRSQLiterstatixrtracklayerrvestS4ArraysS4VectorsscalesselectrshapesnowSparseArraySparseMstringistringrSummarizedExperimentsurvivalsurvminersurvMiscsysTCGAutilstibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsviridisLitevroomwithrxfunXMLxml2xtableXVectoryamlzlibbioczoo

Readme and manuals

Help Manual

Help pageTopics
Change base dir for `.runCache.baseDir
Common call to biomaRt to avoid repetitive code.biomartLoad
Build digest of function from the actual code.buildFunctionDigest
Change cache.compression for run_cache.cacheCompression
Calculate penalty based on data.calcPenalty
Calculate/load result and save if necessary.calculateResult
Calculate combined score for STRINGdb interactions.combinedScore
Create directories for cache.createDirectoryForCache
Workaround for bug with curl when fetching specific ensembl mirror.curlWorkaround
Generic function to calculate degree based on data.degreeGeneric
Default digest method.digestCache
Calculate the upper triu of the matrix.networkGenericParallel
Worker to calculate edge weight for each pair of ixI node and following.networkWorker
Run function and save cache.runCache .runCache,function-method
Saving the cache.saveRunCache
Show messages option in .runCache.showMessage
Temporary directory for runCache.tempdirCache
Write a file in run-cache directory to explain the origin.writeReadme
Create balanced folds for cross validation using stratified samplingbalanced.cv.folds balancedCvFolds
Auxiliary function to generate suitable lambda parametersbuildLambda
Build gene network from peptide idsbuildStringNetwork
Calculate cross validating GLM model with network-based regularizationcv.glmDegree cv.glmHub cv.glmOrphan cv.glmSparseNet
Calculate the degree of the correlation network based on xdatadegreeCor
Calculate the degree of the covariance network based on xdatadegreeCov
Download files to local temporary pathdownloadFileLocal
Retrieve ensembl gene names from biomaRtensemblGeneNames
Retrieve gene names from biomaRtgeneNames
Calculate GLM model with network-based regularizationglmDegree glmHub glmOrphan glmSparseNet
Retrieve hallmarks of cancer count for geneshallmarks
Heuristic function to use in high dimensionsheuristicScale
Heuristic function to penalize nodes with low degreehubHeuristic
Custom pallete of colorsmy.colors myColors
Custom pallete of symbols in plotsmy.symbols mySymbols
Calculates the correlation networknetworkCorParallel
Calculates the covariance networknetworkCovParallel
Setup network optionsnetworkOptions
Heuristic function to penalize nodes with high degreeorphanHeuristic
Retrieve ensembl gene ids from proteinsprotein2EnsemblGeneNames
Separate data in High and Low risk groups (based on Cox model)separate2GroupsCox
Cache of protein-protein network, as it takes some time to retrieve and process this will facilitate the vignette buildingstring.network.700.cache
Download protein-protein interactions from STRING DBstringDBhomoSapiens