dartR (version 0.80)

is.fixed: Test to see 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, t = 0)

Arguments

s1

-- percentage SNP allele frequency for the first population [required]

s2

-- percentage SNP allele frequency for the second population [required]

t

-- threshold value for tollerance 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). Tollerance 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(0,100)
is.fixed(100,0)
is.fixed(80,0)
is.fixed(100,NA)
is.fixed(0,NA)
is.fixed(NA,0)
is.fixed(NaN,100)
is.fixed(NaN,0)
is.fixed(100,NaN)
is.fixed(0,NaN)
is.fixed(NaN,NaN)
is.fixed(NA,NA)
is.fixed(s1=100, s2=0, t=0)
is.fixed(96, 4, t=0.05)

# }