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).

Arcos-Burgos et al.Molecular Biology and Genetic Engineering  2015 3:1DOI : 10.7243/2053-5767-3-1