Covid19AbOmic

The Rscripts folder contains the codes we used for the analysis

The data is contained in the dataset folder

The output folder contains results used for plotting

Covid19AbOmic codes:

1. LassoRF_SVM.R -- This script calculates the AUC (survivors vs non-survivors) for number of replication in a (LASSO+SVM) cross-validation framework.
2. LassoRF_SVM_PermutedModel.R -- This script calculates the AUC (survivors vs non-survivors) for the permuted/shuffled data for number of replication in a (LASSO+SVM) cross-validation framework.
3. Lasso_3_levels.R -- This script calculates the AUC (survivors vs non-survivors vs healthy-control) for number of replication in a (LASSO+SVM) cross-validation framework.
4. Lasso_3_levels_Permuted.R -- This script calculates the AUC (survivors vs non-survivors vs healthy-control) for the permuted/shuffled data for number of replication in a (LASSO+SVM) cross-validation framework.
5. Plot_Box_AUC_fcProfile.R -- This script plots all the actual vs permuted AUC plots
6. Plot_PLS_LassoSelected_Features.R -- This script plots the partial least square regression on the lasso selected features
7. plot_box_ICU_admission.R -- This script plots the distribution of ICU admission of survivors and non-survivors.
8. plot_Other_ARDS.R -- This script plots other ARDS patients LASSO selected features.
9. polarplots coloured by NSSH.r -- This script plots the polarplots of the canonical and non-canonical features.