nuc.div: Nucleotide Diversity

In pegas: Population and Evolutionary Genetics Analysis System

Description

This function computes the nucleotide diversity from a sample of DNA sequences or a set of haplotypes.

Usage

nuc.div(x, ...)
## S3 method for class 'DNAbin'
nuc.div(x, variance = FALSE, pairwise.deletion = FALSE, ...)
## S3 method for class 'haplotype'
nuc.div(x, variance = FALSE, pairwise.deletion = FALSE, ...)

Arguments

x	a matrix or a list which contains the DNA sequences.
variance	a logical indicating whether to compute the variance of the estimated nucleotide diversity.
pairwise.deletion	a logical indicating whether to delete the sites with missing data in a pairwise way. The default is to delete the sites with at least one missing data for all sequences.
...	further arguments to be passed.

Details

This is a generic function with methods for classes "DNAbin" and "haplotype". The first method uses the sum of the number of differences between pairs of sequences divided by the number of comparisons (i.e. n(n - 1)/2, where n is the number of sequences). The second method uses haplotype frequencies. It could be that both methods give (slightly) different results because of missing or ambiguous nucleotides: this is generally solved by setting pairwise.deletion = TRUE.

The variance of the estimated diversity uses formula (10.9) from Nei (1987). This applies only if all sequences are of the same lengths, and cannot be used if pairwise.deletion = TRUE. A bootstrap estimate may be in order if you insist on using the latter option.

Value

A numeric vector with one or two values if variance = TRUE.

Author(s)

Emmanuel Paradis

References

Nei, M. (1987) Molecular evolutionary genetics. New York: Columbia University Press.

See Also

base.freq, GC.content, theta.s, seg.sites

Examples

data(woodmouse)
nuc.div(woodmouse)
nuc.div(woodmouse, TRUE)
nuc.div(woodmouse, FALSE, TRUE)

Example output

Loading required package: ape
Loading required package: adegenet
Loading required package: ade4

   /// adegenet 2.1.1 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

[1] 0.0129461
[1] 1.294610e-02 4.820826e-05
[1] 0.01316744

pegas documentation built on Dec. 16, 2021, 5:09 p.m.