SensitivityAnalysis.R

SensitivityAnalysis.R

SensitivityAnalysis.R is a script that simulates the model under various knockouts of components and inhibitions of reactions, monitoring their effects on a given set of output nodes.

Running

Run SensitivityAnalysis.R by sourcing it directly (./SensitivityAnalysis.R) or with Rscript (Rscript ./SensitivityAnalysis.R).

Parameters should be set in a config file (SensitivityAnalysis.R /path/to/config.R, see below for config file format).

Parameters

• file: Path of local master rxncon file
• driveFile: File name or path of master rxncon file (on Google Drive)
• modules: Comma-separated modules to be loaded from master rxncon file [default: load all modules]
• minQuality: Minimum quality for rule to be loaded [default: 0]
• out: Folder to which output files will be written [default: ./out/]
• ligands: Comma-separated rxncon name(s) of ligand component(s) to be toggled in simulation
• inhib: Comma-separated rxncon name(s) of node(s) to always be inhibited in simulation. Useful for test synergistic effects of inhibition
• outputs: Comma-separated rxncon name(s) of node(s) to be considered as outputs when performing sensitivity analysis

Config file

Config files should be .R files following this general format:

config <- list(
	arg1 = "string value",
	arg2 = FALSE,
	arg3 = 23
	...
)

Output

SensitivityAnalysis.R will output the following files:

• master.xlsx: rxncon file downloaded from Google Drive
• modules.xlsx: rxncon file containing only the modules loaded by SensitivityAnalysis.R
• modules.boolnet, modules_initial_vals.csv, modules_symbols.csv: BoolNet files generated by rxncon2boolnet.py
• no_ligand_KO_analysis.csv, no_ligand_KO_analysis.pdf, ligand_KO_analysis.csv, ligand_KO_analysis.pdf: Files showing effect of component knockout both with and without ligand.
• no_ligand_reaction_analysis.csv, no_ligand_reaction_analysis.pdf, ligand_reaction_analysis.csv, ligand_reaction_analysis.pdf: Files showing effect of reaction inhibition both with and without ligand.