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Last data update: 2014.03.03

R: P-values and Linkage Disequilibrium measures for several...

LD2sided.pvals

R Documentation

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
`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

Examples

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

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(LDtests)
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/LDtests/LD2sided.pvals.Rd_%03d_medium.png", width=480, height=480)
> ### Name: LD2sided.pvals
> ### Title: P-values and Linkage Disequilibrium measures for several tests
> ###   of Linkage Disequilibrium
> ### Aliases: LD2sided.pvals
> ### Keywords: htest
> 
> ### ** Examples
> 
> ctable <- c(0,9,5,16)
> LD2sided.pvals(ctable)
$pval.cond
[1] 0.2741935

$pval.Fish
[1] 0.2860301

$pval.LR
[1] 0.1622458

$pval.r
[1] 0.2860301

$pval.Dprime
[1] 0.1436782

$pval.delta
[1] 0.1622458

$pval.Q
[1] 0.1436782

$Prob
[1] 0.142794

$LR
[1] 3.980948

$r
[1] -0.29277

$Dprime
[1] -1

$delta
[1] -0.5625

$Q
[1] -1

$yobs
[1] 0

$n1
[1] 9

$n2
[1] 5

$nn
[1] 30

> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>