R: An internal function to tests if two populations are fixed at...

utils.is.fixed {dartR.base}

R Documentation

An internal function to tests if two populations are fixed at a given locus

Description

WARNING: UTILITY SCRIPTS ARE FOR INTERNAL USE ONLY AND SHOULD NOT BE USED BY END USERS AS THEIR USE OUT OF CONTEXT COULD LEAD TO UNPREDICTABLE OUTCOMES.

Usage

utils.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

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

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)

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