View source: R/nucleotideDiversity.R
nucleotideDiversity | R Documentation |
Calculate nucleotide diversity for set of sequences. Note that
this is NOT Nei's nucleotide diversity
(usually referred to as π). Nei's π is the mean number
of nucleotide differences between sequences. See
nucleotideDivergence
for this value.
nucleotideDiversity(x, bases = c("a", "c", "g", "t"), simplify = TRUE)
x |
a set of sequences or a gtypes object with sequences. |
bases |
nucleotides to consider when calculating diversity. |
simplify |
if |
Vector of diversity of nucleotides by site.
Eric Archer eric.archer@noaa.gov
data(dloop.g) nd <- nucleotideDiversity(dloop.g) quantile(nd)
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