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Table 1 Table representing the results of the benchmark on the EMT test dataset (A) and on the GM12878 test dataset (B) using a threshold for the PSI values and IR ratios of 0.10

From: IRFinder-S: a comprehensive suite to discover and explore intron retention

Method Excl. TP TN FP FN TPR TNR PPV Acc. FDR
A. EMT test results
 IRFinder 25989 695 95198 428 138 0.83 0.99 0.62 0.98 0.38
 IRFinder-S 25989 673 35515 111 160 0.81 1.00 0.86 0.99 0.14
 iREAD 28221 18 33994 86 129 0.12 1.00 0.17 0.99 0.83
 Whippet 59822 443 1978 87 118 0.79 0.96 0.84 0.92 0.16
 MAJIQ 30179 388 29572 1951 358 0.52 0.94 0.17 0.93 0.83
B. GM12878 test results
 IRFinder 30943 1228 50720 729 185 0.87 0.99 0.63 0.98 0.37
 IRFinder-S 30943 1077 51123 326 336 0.76 0.99 0.77 0.99 0.23
 iREAD 37905 71 45501 179 149 0.32 1.00 0.28 0.99 0.72
 Whippet 80125 772 2459 347 102 0.88 0.88 0.69 0.88 0.31
 MAJIQ 50932 826 30626 917 504 0.62 0.97 0.47 0.96 0.53
  1. Excl intron excluded, TP true positive, TN true negative, FP false positive, FN false negative, TPR true positive rate (sensitivity), TNR true negative rate (specificity), PPV positive predicted value (precision), Acc. accuracy, FDR false discovery rate