R:
>install.packages('deSolve')
>install.packages('pracma')
>install.packages('minpack.lm')
>install.packages('plotrix')
>install.packages('gridExtra)
>install.packages('ggplot2')
to run all analyses, you have just to run the following command inside the src folder: Rscript ./main_VdP_V01_revision.R
This script will compute all statistics and make plots
This script expects a folder structure like this to run:
* ./src : contains all scripts
* ./results : will contain all performance tables and plots
* ./results/paper/ : will contain all paper tables and plots
* ./data : will contain all input tables
These are Input needed:
* input tables in ./data
Running the script these Output files will be generated in ./results
* table with fmut optimized (HDL, LDL)
* table with fmut optimized (TC), only for DHCR7 gene
* boxplot of cholesterol levels (training set)
* table with difference between predicted and experimental cholesterol
* table with trained vs van de Pas et al. fmut
* sensitivity analysis plot (HDL, LDL, TC)
* barplot with HDL levels (predicted, real)
* table with HDL levels (predicted, real)
* barplot with LDL levels (predicted, real)
* table with LDL levels (predicted, real)
* table with number of mutations and patients for each gene
* percentage of difference between predicted and experimental
* barplot with TC levels (predicted, real)
* table with predicted and real blood cholesterol values
* table with PCC, KCC, RMSD and Rsquared of predicted blood cholesterol values
* table with TC levels (predicted, real)
* table with standard deviation of model predictions
* table with bootstrap