Network Analysis Supported by Boosting

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Documentation for package ‘netboost’ version 2.12.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

.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)