Scripts ro run in silico model for cholesterol level prediction

REQUIREMENTS

R:
>install.packages('deSolve')
>install.packages('pracma')
>install.packages('minpack.lm')
>install.packages('plotrix')
>install.packages('gridExtra)
>install.packages('ggplot2')

USAGE

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