LD2sided.pvals: P-values and Linkage Disequilibrium measures for several...

In LDtests: Exact tests for Linkage Disequilibrium and Hardy-Weinberg Equilibrium

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
LR	Likelihood ratio statistic
r	Correlation coefficient
Dprime	D prime
delta	delta (Devlin and Risch)
Q	Yule's Q
yobs	The observed n11 (first cell in the table)
n1	Row margin
n2	Column margin
nn	Sample size

Author(s)

Alex Lewin

References

Kulinskaya and Lewin 2008

See Also

LD2sided.tables

Examples

ctable <- c(0,9,5,16)
LD2sided.pvals(ctable)

LDtests documentation built on May 2, 2019, 2:44 p.m.