variableSites: Variable Sites
Description
Identify variable sites among sequences.
Usage
variableSites(x, bases = c("a", "c", "g", "t", "-"), simplify = TRUE)
Arguments
x
a '>gtypes object with sequences,
a DNAbin
object, or a list of sequences.
bases
character vector of bases to consider.
simplify
if there is a single locus, return result in a simplified
form? If FALSE
a list will be returned wth one element per locus.
Value
A list with:
- site
a DNAbin
object composed of variable sites.
- site.freqs
a matrix of base pair frequencies by site.
Examples
Run this code# NOT RUN {
data(dolph.haps)
variableSites(dolph.haps)
# }
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