is.fixed: Tests if two populations are fixed at a given locus

In green-striped-gecko/dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Tests if two populations are fixed at a given locus

Description

This script compares two percent allele frequencies and reports TRUE if they represent a fixed difference, FALSE otherwise.

Usage

is.fixed(s1, s2, tloc = 0)

Arguments

s1	Percentage SNP allele or sequence tag frequency for the first population [required].
s2	Percentage SNP allele or sequence tag frequency for the second population [required].
tloc	Threshold value for tolerance in when a difference is regarded as fixed [default 0].

Details

A fixed difference at a locus occurs when two populations share no alleles, noting that SNPs are biallelic (ploidy=2). Tolerance in the definition of a fixed difference is provided by the t parameter. For example, t=0.05 means that SNP allele frequencies of 95,5 and 5,95 percent will be reported as fixed (TRUE).

Value

TRUE (fixed difference) or FALSE (alleles shared) or NA (one or both s1 or s2 missing)

Author(s)

Custodian: Arthur Georges (bugs? Post to https://groups.google.com/d/forum/dartr)

See Also

gl.fixed.diff

Examples

is.fixed(s1=100, s2=0, tloc=0)
is.fixed(96, 4, tloc=0.05)

green-striped-gecko/dartR documentation built on Sept. 7, 2024, 4:15 a.m.