View source: R/site.spectrum.R
site.spectrum  R Documentation 
site.spectrum
computes the (un)folded site frequency spectrum
of a set of aligned DNA sequences or SNPs.
site.spectrum(x, ...) ## S3 method for class 'DNAbin' site.spectrum(x, folded = TRUE, outgroup = 1, ...) ## S3 method for class 'loci' site.spectrum(x, folded = TRUE, ancestral = NULL, ...) ## S3 method for class 'spectrum' plot(x, col = "red", main = NULL, ...)
x 
a set of DNA sequences (as an object of class

folded 
a logical specifying whether to compute the folded site
frequency spectrum (the default), or the unfolded spectrum if

outgroup 
a single integer value giving which sequence is
ancestral; ignored if 
ancestral 
a vector of ancestral alleles (required if

col 
the colour of the barplot (red by default). 
main 
a character string for the title of the plot; a generic
title is given by default (use 
... 
further arguments passed to

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 ith 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.
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.
Emmanuel Paradis
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)
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