Redraw the resulting ROC curve once analyzed.

Redraw the resulting ROC curve once analyzed.

Usage

MOVA_redraw(MOVA_predict_orig_file, col, add = FALSE)

Arguments

MOVA_predict_orig_file

"protein/gene name_Target or Pathogenic_predict_orig.csv" output by the MOVA function, or csv file for MOVA_redraw output by each function

col

Color of ROC curve

add

When TRUE, it overlays an existing graph; when FALSE, it creates a new graph.

Details

Value

References

Author

Yuya Hatano

Note

See also

Examples

Hgmd_divide("./source/TARDBP.csv")
Edit_gnomAD_file("./source/gnomAD_v3.1.2_ENST00000240185_2023_02_14_13_23_48.csv", "./source/TARDBP_gnomAD.csv")
Edit_variant_data("../CADD_REVEL/AlphScore_final.tsv", "./source/TARDBP.csv", "./source/TARDBP_gnomAD.csv", "Q13148", "TARDBP", "./source/TARDBPvariantdata.csv")
Edit_polyphen_data("../dbNSFP/dbNSFP4.3a/dbNSFP4.3a_variant.chr1","./source/TARDBPvariantdata.csv", "TARDBP_alph.csv",  "Q13148",  11012654, 11025492 ,"./source/TARDBPvariantdatapol.csv", "./source/TARDBP_alphpol.csv")
Edit_final_variant_file("./source/TARDBP_alphpol.csv","./source/TARDBP_alphpol2.csv")
MOVA("./source/Q13148.fa", "TARDBP", "./source/AF-Q13148-F1-model_v2.pdb","./source/TARDBP_alphpol2.csv", "./source/TARDBPvariantdatapol.csv")
MOVA_SVM("TARDBP", "TARDBP_Target_finalpredict.csv","TARDBP_Target_predict.csv")
MOVA_xgboost("TARDBP", "TARDBP_Target_finalpredict.csv","TARDBP_Target_predict.csv")
MOVA_redraw("TARDBP_Target_predict_orig.csv",col="red")
PolyPhen_MOVA("TARDBP_Target_predict.csv")
AlphScore_MOVA("TARDBP_Target_predict.csv")
CADD_MOVA("TARDBP_Target_predict.csv")
REVEL_MOVA("TARDBP_Target_predict.csv")
EVE_MOVA("TARDBP_Target_predict.csv", "../dementia/EVE_all_data/variant_files/TADBP_HUMAN.csv")
MOVA_redraw("TARDBP_Target_predict_orig.csv",col="red")
MOVA_redraw("TARDBP_Target_predict_orig_SVM.csv",col="black", add=TRUE)
MOVA_redraw("TARDBP_Target_predict_orig_xgboost.csv",col="blue", add=TRUE)

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--  or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (MOVA_predict_orig_file, col, add = FALSE) 
{
    df <- fread(MOVA_predict_orig_file)
    out <- cvAUC(df$predict, df$result, label.ordering = NULL, 
        folds = df$iter3)
    plot(out$perf, col = col, avg = "vertical", add = add)
  }
#> function (MOVA_predict_orig_file, col, add = FALSE) 
#> {
#>     df <- fread(MOVA_predict_orig_file)
#>     out <- cvAUC(df$predict, df$result, label.ordering = NULL, 
#>         folds = df$iter3)
#>     plot(out$perf, col = col, avg = "vertical", add = add)
#>   }
#> <environment: 0x0000011a8aa4b630>