# nuc.div

0th

Percentile

##### Nucleotide Diversity

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

Keywords
manip, univar
##### Usage
nuc.div(x, ...)
# S3 method for DNAbin
nuc.div(x, variance = FALSE, pairwise.deletion = FALSE, ...)
# S3 method for 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.

##### References

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

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

##### Aliases
• nuc.div
• nuc.div.DNAbin
• nuc.div.haplotype
##### Examples
# NOT RUN {
data(woodmouse)
nuc.div(woodmouse)
nuc.div(woodmouse, TRUE)
nuc.div(woodmouse, FALSE, TRUE)
# }

Documentation reproduced from package pegas, version 0.12, License: GPL (>= 2)

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