nuc.div | R Documentation |
This function computes the nucleotide diversity from a sample of DNA sequences or a set of haplotypes.
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, ...)
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. |
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.
A numeric vector with one or two values if variance = TRUE
.
Emmanuel Paradis
Nei, M. (1987) Molecular evolutionary genetics. New York: Columbia University Press.
base.freq
, GC.content
,
theta.s
, seg.sites
data(woodmouse)
nuc.div(woodmouse)
nuc.div(woodmouse, TRUE)
nuc.div(woodmouse, FALSE, TRUE)
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