Microsatellite markers

Allele frequencies of multi-allelic markers (such as microsatellites) in two reference groups, for hybrid_scores_microsat() and for simulating reference histories (microsat in simulate_hybrid_zone() and build_reference()). Microsatellites rarely have alleles fixed between species, so each animal's hybrid index and interspecies heterozygosity are estimated by likelihood from these frequencies.

Usage

microsat_markers(alleles, groups, ref1, ref2, prior = 0.5)

Arguments

alleles

Integer matrix of allele sizes, two columns per locus (named locus.a1, locus.a2), animals in rows; NA for missing.

groups

Group label of each animal.

ref1, ref2

Labels of the two reference groups.

prior

Pseudo-count added to every allele seen in either group, so that an allele absent from one reference sample is rare, not impossible, in that species.

Value

A list with loci (locus names), alleles (per locus, the allele sizes), and freq1, freq2 (per locus, their frequencies in each reference group).

Examples

set.seed(1)
a <- cbind(L1.a1 = c(rep(100, 10), rep(104, 10)), L1.a2 = c(rep(100, 10), rep(104, 10)))
ms <- microsat_markers(a, rep(c("sp1", "sp2"), each = 10), "sp1", "sp2")
ms$freq1
#> $L1
#> [1] 0.97619048 0.02380952
#>