site.spectrum computes the (un)folded site frequency spectrum
of a set of aligned DNA sequences or SNPs.
site.spectrum(x, ...)
# S3 method for DNAbin
site.spectrum(x, folded = TRUE, outgroup = 1, ...)
# S3 method for loci
site.spectrum(x, folded = TRUE, ancestral = NULL, ...)
# S3 method for spectrum
plot(x, col = "red", main = NULL, ...)site.spectrum returns an object of class "spectrum"
which is a vector of integers (some values may be equal to zero) with
the attributes "sample.size" and "folded" (a logical
value) indicating which version of the spectrum has been computed.
a set of DNA sequences (as an object of class
"DNAbin"), or an object of class "spectrum".
a logical specifying whether to compute the folded site
frequency spectrum (the default), or the unfolded spectrum if
folded = FALSE.
a single integer value giving which sequence is
ancestral; ignored if folded = TRUE.
a vector of ancestral alleles (required if
folded = FALSE), typically from an output of
VCFloci.
the colour of the barplot (red by default).
a character string for the title of the plot; a generic
title is given by default (use main = "" to have no title).
further arguments passed to
barplot, or to other mehods.
Emmanuel Paradis
Under the infinite sites model of mutation, mutations occur on distinct sites, so every segregating (polymorphic) site defines a partition of the \(n\) sequences (see Wakeley, 2009). The site frequency spectrum is a series of values where the \(i\)th element is the number of segregating sites defining a partition of \(i\) and \(n - i\) sequences. The unfolded version requires to define an ancestral state with an external (outgroup) sequence, so \(i\) varies between 1 and \(n - 1\). If no ancestral state can be defined, the folded version is computed, so \(i\) varies between 1 and \(n/2\) or \((n - 1)/2\), for \(n\) even or odd, respectively.
If folded = TRUE, sites with more than two states are ignored
and a warning is returned giving how many were found.
If folded = FALSE, sites with an ambiguous state at the
external sequence are ignored and a warning is returned giving how
many were found. Note that it is not checked if some sites have more
than two states.
If x is an object of class "loci", the loci which are
not biallelic (e.g., SNPs) are dropped with a warning.
Wakeley, J. (2009) Coalescent Theory: An Introduction. Greenwood Village, CO: Roberts and Company Publishers.
DNAbin for manipulation of DNA sequences in R,
haplotype
require(ape)
data(woodmouse)
(sp <- site.spectrum(woodmouse))
plot(sp)
Run the code above in your browser using DataLab