# Network Analysis Supported by Boosting

## Documentation for package ‘netboost’ version 1.0.0

- 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_tranfer | Transfer of Netboost clustering to new data.
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)