LD2sided.pvals: P-values and Linkage Disequilibrium measures for several tests of Linkage Disequilibrium
Description
Calculates 2-sided LD tests based on different measures of LD (Kulinskaya and Lewin 2008), 1-sided Fisher's exact test for LD and the conditional p-values proposed in Kulinskaya (2008) to overcome the problems of asymetric distributions.
Usage
LD2sided.pvals(ctable)
Arguments
ctable
Vector of the 4 entries in the 2x2 contingency table
Value
pval.cond
Conditional p-value
pval.Fish
Fisher's p-value (sum of tables less probable than observed)
pval.LR
P-value based on the likelihood ratio statistic
pval.r
P-value based on the correlation coefficient
pval.Dprime
P-value based on D prime
pval.delta
P-value based on delta (Devlin and Risch)
pval.Q
P-value based on Yule's Q
Prob
Probability under the null hypothesis of the observed table