This repository contains all the R scrips used for the assessment of the CAGI-3 "p16 challenge".
All the scripts can be reused for performance assessment of bioinformatics tools to predict phenotypic effects of genetic variants of unknown significance (VUS).
The analysis requires the following R packages to be installed
Each script can be run from a terminal as the example below
Rscript 1_main_numerical_assessment.R
In this section a brief description of each script is given
| Script | Description |
|---|---|
| 1 | calculates the main numerical measures (i.e. correlations, AUC, RMSD).In additions it produces the tables needed by other scripts to generate assessment figures and tables. |
| 2 | calculates correlation measure among all predictions and produce an heatmap figure to visualize results |
| 3 | calculates correlation measure among performance indices and produce an heatmap figure to visualize results |
| 4 | calculates the pairwise significance of challenge evaluations and produce an heatmap figure |
| 5 | draws experimental values versus predicted values graph |
| 6 | calculates only PSWD10 and produce a table to identify difficut targets |