gl.fixed.diff: Generate a matrix of fixed differences from a genelight or genind object {adegenet}

Description

This script takes SNP data grouped into populations in a genlight object (DArTSeq) and generates a matrix of fixed differences between populations taken pairwise

Usage

gl.fixed.diff(gl, tloc = 0, nlimit = 2, pc = FALSE, v = 1)

Arguments

-- name of the genlight object containing SNP genotypes or a genind object containing presence/absence data [required]

tloc

-- threshold defining a fixed difference (e.g. 0.05 implies 95:5 vs 5:95 is fixed) [default 0]

nlimit

-- number of individuals with non-missing SNP scores in the two populations combined, required for scoring of fixed differences [default 2]

-- logical value indicating whether to report fixed difference counts (pc=FALSE) or percentages (pc=TRUE) [default TRUE]

-- verbosity = 0, silent; 1, brief; 2, verbose [default 1]

Value

Matrix of percent fixed differences (lower matrix), number of loci (upper matrix)

Details

A fixed difference at a locus occurs when two populations share no alleles. The challenge with this approach is that when sample sizes are finite, fixed differences will occur through sampling error, compounded when many loci are examined. Simulations suggest that sample sizes of n1=5 and n2=5 is adequate to reduce the probability of [experiment-wide] type 1 error to negligible levels [ploidy=2]. A warning is issued if comparison between two populations involves sample sizes less than 5, taking into account allele drop-out. The minimum sample size for scoring fixed differences between two populations can be set with the parameter nlimit. An absolute fixed difference is as defined above. However, one might wish to score fixed differences at some lower level of allele frequency difference, say where percent allele fequencies are 95,5 and 5,95 rather than 100:0 and 0:100. This adjustment can be done with the tloc parameter. For example, tloc=0.05 means that SNP allele frequencies of 95,5 and 5,95 percent will be regarded as fixed when comparing two populations at a locus.

Examples

Run this code

# NOT RUN {
#only used the first 20 individuals due to runtime reasons 
mat <- gl.fixed.diff(testset.gl[1:20,], tloc=0.05, nlimit=5)
# }