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

1

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

1
2
ctable <- c(0,9,5,16)
LD2sided.pvals(ctable)