dartR (version 2.0.4)

is.fixed: 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].

Value

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

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).

See Also

gl.fixed.diff

Examples

# NOT RUN {
is.fixed(s1=100, s2=0, tloc=0)
is.fixed(96, 4, tloc=0.05)
# }