Tutorial:
- File Tutorial_bnClustOmics.pdf contains two examples on how to perform clustering using the package bnClustOmics
- File Tutorial_bnClustOmics.R contains the code from this tutorial as an R script
Simulations:
- File simulations1.R contains the code that can be used to replicate simulations (parallelised) depicted in Figures 2A:C; help functions for data generation and application of different clustering algorithms are sourced from the folder simulations_code
- File simulations2.R contains the code the code that can be used to replicate simulations (parallelised) depicted in Figure 2D; help function for data generation and application of different clustering algorithms are sourced from the folder simulations_code
- File simulations3 contains the code for simulations (parallelised) depicted in Figure 3A:C; help functions for data generation and application of different clustering algorithms are sourced from the folder simulations_code
HCC clustering:
- File HCC_prior.R contains the code that was used for constructing blacklist and penalization matrices based on STRING interactions and their scores. It also shows the comparison between STRING and BIOGRID interactions. This file needs files from the folder DBdata.
- File HCCclustering contains code of network-based clustering of HCC data with bnClustOmics
- File HCCfullclustering.R contains code for clustering with other algorithms shown
- The functions needed for the analysis of the results (Cox model etc) are contained in the file helpresfns.R
Data
- Folder HCCinputs contains .rds file with pre-constructed objects needed to run the clustering
- Folder simulation_results contains dataframes with the results of running corresponding scripts (simulation1-simulation3)
- Folder HCCresults contains the files with the results of applying bnClustOmics to the HCC data