Description Usage Arguments Value Note Author(s) References Examples
This function tests the neutral mutation hypothesis with Tajima's D.
1 | tajima.test(x)
|
x |
a set of DNA sequences (object of class |
A list with three numeric values:
D |
Tajima's D statistic. |
Pval.normal |
the p-value assuming that D follows a normal distribution with mean zero and variance one. |
Pval.beta |
the p-value assuming that D follows a beta distribution after rescaling on [0, 1] (Tajima, 1989). |
Alignment gaps in the sequences are ignored when calculating pairwise distances.
Emmanuel Paradis
Tajima, F. (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 595–595.
1 2 3 | require(ape)
data(woodmouse)
tajima.test(woodmouse)
|
Loading required package: ape
Loading required package: adegenet
Loading required package: ade4
/// adegenet 2.0.1 is loaded ////////////
> overview: '?adegenet'
> tutorials/doc/questions: 'adegenetWeb()'
> bug reports/feature requests: adegenetIssues()
Attaching package: 'pegas'
The following object is masked from 'package:ade4':
amova
The following object is masked from 'package:ape':
mst
$D
[1] -1.365449
$Pval.normal
[1] 0.1721118
$Pval.beta
[1] 0.1747609
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