Network Centrality Metrics for Elastic-Net Regularized Models

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Documentation for package ‘glmSparseNet’ version 1.6.0

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.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
buildLambda Auxiliary function to generate suitable lambda parameters
buildStringNetwork Build gene network from peptide ids
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
degreeSparsebn Calculate degree of correlation matrix
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
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
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