########### Scripts for CAGI 5 PCM1 challenge assessment ##################
R:
>install.packages('ROCR')
>install.packages('plotrix')
>install.packages('ggthemes')
>install.packages('ggplot2')
to run all analyses, you have just to run the following command: Rscript ./src/CAGI_assessment_main.R This script will check submission format, computes all statistics and makes plots This script expects a folder structure like this to run: ./src <- contains all scripts ./results <- will contain all performance tables and plots ./data <- has to contain 3 folders: experimental_value, submissions, template
These are Input needed:
# experimental values file in ./data/experimental_value
# submission template in ./data/template
# submission files in ./data/submissions
Running the script these Output files will be generated in ./results
# confusion matrix of each submission
# heatmap of Correlation among submissions (MO or MO+WT p value)
# heatmap containing all performance indices (BACC, MCC, F1, TPR, TNR)
# plot with percentage of correct predictions for each variant
# scatterplot with all submissions p value and SD (MO or MO+WT p value)
# plots of the distribution of BACC/F1/MCC values of random predictions
# table containing all performance indices (BACC, MCC, F1, TPR, TNR)
# table containing prediction rank for all performance indices (BACC, MCC, F1, TPR, TNR)
# table with performance index and rank
# table with one confusion matrix for each submission