Function reference
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AlphScore_MOVA() - Function to compare MOVA and AlphScore.
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CADD_AlphScore() - Function to compare MOVA and CADD + AlphScore.
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CADD_MOVA() - Function to compare MOVA and CADD.
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Com_CADD_MOVA() - Combining CADD and MOVA
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Com_REVEL_MOVA() - Combining REVEL and MOVA
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Edit_final_variant_file() - Creating files for MOVA function input
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Edit_gnomAD_file() - Function to retrieve the required information from the downloaded gnomAD file
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Edit_polyphen_data() - This function adds PolyPhen-2 predictions to the MOVA input file.
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Edit_variant_data() - Integrate HGMD file and gnomAD file.
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EVE_Final() - Add the predicted value of EVE for each variant.
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EVE_MOVA() - Function to compare MOVA and EVE.
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Hgmd_divide() - Creation of Hgmd files
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MOVA() - Derivation of predictions and ROC curves by MOVA
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MOVA_3d_distance() - MOVA with 'distance to the known pathogenic variant' learned instead of position coordinates
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MOVA_3d_distance_log() - logistic analysis with 'distance to the known pathogenic variant' learned instead of position coordinates
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MOVA_LOPOV() - do a leave one protein out validation (using 11 proteins' variations for training, 1 protein's for testing)
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MOVA_only_3d_coordinates() - MOVA with only 3D coordinates as explanatory variable
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MOVA_only_3d_distance() - A simple baseline approach based on distance to the known pathogenic variants
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MOVA_only_BLOSUM62() - MOVA with only BLOSUM62 as explanatory variable.
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MOVA_only_pLDDT() - MOVA with only pLDDT as explanatory variable.
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MOVA_plus_3d_distance() - Add 'distance to the known pathogenic variant' as an explanatory variable to the MOVA.
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MOVA_plus_3d_distance_SVM() - Add 'distance to the known pathogenic variant' to the explanatory variables of MOVA and train with SVM.
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MOVA_plus_3d_distance_xgboost() - Add 'distance to the known pathogenic variant' to the explanatory variables of MOVA and train with XGBoost.
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MOVA_predistance() - Calculate the 'distance to the known pathogenic variant' for each variant in MOVA_final_predict_file.
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MOVA_redraw() - Redraw the resulting ROC curve once analyzed.
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MOVA_SVM() - The training was performed in SVM.
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MOVA_without_3d_coordinates() - MOVA with pLDDT and BLOSUM62 as explanatory variable
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MOVA_xgboost() - The training was performed in XGBoost.
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PolyPhen_MOVA() - Function to compare MOVA and PolyPhen-2.
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REVEL_AlphScore() - Function to compare MOVA and REVEL + AlphScore.
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REVEL_MOVA() - Function to compare MOVA and REVEL.
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variant_predict_plot() - The predicted probability of pathogenicity was compared between MOVA and PolyPhen-2.