nucleotideDiversity: Nucleotide Diversity

In EricArcher/strataG: Summaries and Population Structure Analyses of Genetic Data

Nucleotide Diversity

Description

Calculate nucleotide diversity for set of sequences. Note that this is NOT Nei's nucleotide diversity (usually referred to as \pi). Nei's \pi is the mean number of nucleotide differences between sequences. See nucleotideDivergence for this value.

Usage

nucleotideDiversity(x, bases = c("a", "c", "g", "t"), simplify = TRUE)

Arguments

x	a set of sequences or a gtypes object with sequences.
bases	nucleotides to consider when calculating diversity.
simplify	if TRUE and only one loci exists, return a vector, otherwise, a list of vectors with one element per locus will be returned.

Value

Vector of diversity of nucleotides by site.

Author(s)

Eric Archer [e-mail]

Examples

data(dloop.g)

nd <- nucleotideDiversity(dloop.g)
quantile(nd)

EricArcher/strataG documentation built on May 17, 2024, 12:41 p.m.