dartR.base (version 1.0.5)

utils.is.fixed: 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)

Value

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

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].

Author

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

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).

See Also

gl.fixed.diff

Other utilities: gl.alf(), utils.check.datatype(), utils.collapse.matrix(), utils.dart2genlight(), utils.dist.binary(), utils.flag.start(), utils.hamming(), utils.het.pop(), utils.impute, utils.jackknife(), utils.n.var.invariant(), utils.plot.save(), utils.read.fasta(), utils.read.ped(), utils.recalc.avgpic(), utils.recalc.callrate(), utils.recalc.freqhets(), utils.recalc.freqhomref(), utils.recalc.freqhomsnp(), utils.recalc.maf(), utils.reset.flags(), utils.transpose(), utils.vcfr2genlight.polyploid()