Network Analysis Supported by Boosting


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Documentation for package ‘netboost’ version 2.4.1

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.onAttach Package startup: used to fetch installation path of the own package, as required for executing binary programs delivered with it.
calculate_adjacency Calculate network adjacencies for filter
cpp_dist_tom Function to calcutate distance
cpp_filter_base Initialise boosting with chosen accelerator hardware (x86, AVX, FMA)
cpp_filter_end Boosting cleanup (required to free memory)
cpp_filter_step Single boosting step
cpp_tree_search Tree search.
cut_dendro Module detection for an individual tree
cut_trees Module detection for the results from a nb_mcupgma call
mcupgma_exec Execute a program/script from the installed MCUPGMA suite.
nb_clust Netboost clustering step
nb_dist Calculate distance (external wrapper for internal C++ function) Parallelisation inside C++ program with RcppParallel.
nb_filter Boosting via C++ function. Parallelisation by R-package parallel with forking (overhead of this method does not fall into account as single steps are ~10s).
nb_mcupgma Calculate dendrogram for a sparse distance matrix (external wrapper MC-UPGMA clustering package Loewenstein et al.
nb_moduleEigengenes Netboost module aggregate extraction.
nb_plot_dendro Plot dendrogram from Netboost output.
nb_summary Summarize results from a forest. Plot trees together.
nb_transfer Transfer of Netboost clustering to new data.
netboost Netboost clustering.
netboostMCUPGMAPath Returns the absolute path to folder with mcupgma executables and scripts.
netboostPackagePath Returns the absolute path to "exec" folder in the package.
netboostTmpCleanup Cleans the netboost temporary folder. This can be useful during the session as mcupgma creates vast directory structures (for iterations). Creates the own folder (all netboost temporary data is stored in netboostTmpPath(), which is equal to tempdir()/netboost). Also used for first time setup of folder.
netboostTmpPath Returns the absolute path to temporary folder of the package. To change temporary path, use normal R variables (TEMPDIR etc).
tcga_aml_meth_rna_chr18 TCGA RNA and methylation measurement on a subset of chromosome 18 for 80 AML patients.
tree_dendro Calculate the dendrogram for an individual tree
tree_search Extracts independent trees from nb_mcupgma results (external wrapper for internal C++ function)