The permutation p-value for a particular protein is the proportion of the permutations in which the permuted test statistic exceeds the observed test statistic in absolute values.
Calculate θ perm =|R O −R P |, the permuted test statistic, based on the permuted data.
By counting how often the observed test statistic exceeds the permuted test statistic, one can estimate a permutation test p-value.
Let the p-value be the fraction of times that the permuted test statistic is greater than the observed test statistic; p-value (= frac {text {# of times }theta _{perm} > theta _{obs}}{text {# of permutations}}). .
The results suggest that correlations between TS, CS and GR are about 2.2 and 1.5 fold of the maximum permuted coefficients, demonstrating that such modest correlations are still significant (P<0.0001) (Text S1, Figure S2).
p values were calculated as the proportion of permuted test statistics that are greater than the real test statistic.
Our standardization is against 1000 permuted test statistics at the same locus in the same LD background.
Probabilities for permuted tests were calculated by asymptotic inference.
*P-values were obtained by permutation test on 10,000 permuted sample.
The regression model is fit by aligning a set of query maps to a single permuted reference map, avoiding the computational bottleneck of performing a permutation test for each aligned query map against a set of permuted reference maps.
