Tests if two populations are fixed at a given locus

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).

Author

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

Examples

is.fixed(s1=100, s2=0, tloc=0)
#> [1] 1
is.fixed(96, 4, tloc=0.05)
#> [1] 1