Table 1 : Results and expressions for calculating the performance measures used to
quantitatively compare prGWAS and GWAS.
Table 1a | ||
prGWAS | GWAS | |
Significant | Not significant | |
Significant | a | b |
Not significant | c | d |
Table 1b | ||
Measure | Expression | |
Sensitivity | a/(a+c) | |
Specificity | d/(c+d) | |
Positive predictive value (PPV) | a/(a+b) | |
Negative predictive value (NPV) | d/(c+d) | |
False discovery rate (FDR) | 1-PPV | |
False negatives rate (FNR) | 1-NPV | |
Classification rate (CR) | (a+d)/(a+b+c+d) | |
Lift | a(a+b+c+d)/{(a+b)(a+c)} | |
(a) Possible results when the GWAS and prGWAS are compared. Here, a is the number of significant
markers found by both methods, b is the number of positive SNPs according to prGWAS but not positive
according to GWAS, c corresponds to those markers not found to be significant by prGWAS but that are
true positives according to GWAS, and d is the number of SNPs labeled as not significant by both methods;
(b) expressions for calculating the performance measures used to quantitatively compare prGWAS and
GWAS (see the Methods).