Check that markers are diagnostic in the parents that actually bred

Markers chosen in reference samples can still be shared by the animals that founded a hybrid population, for example when a release strain or cross parent differs from the reference sample. First-generation hybrids expose such markers: at a truly diagnostic marker every F1 is heterozygous. This function finds animals that look like F1s (hybrid index near 0.5 and high interspecies heterozygosity) and reports, for each marker, how often they are heterozygous there.

Usage

check_markers(
  geno,
  markers,
  scores,
  S_range = c(0.4, 0.6),
  min_H = 0.7,
  flag = 0.7
)

Arguments

geno

Genotype matrix as in diagnostic_markers().

markers

Output of diagnostic_markers().

scores

Output of hybrid_scores() for the same animals.

S_range

Range of hybrid index for likely F1s.

min_H

Smallest interspecies heterozygosity for likely F1s.

flag

Markers heterozygous in fewer than this share of likely F1s are flagged.

Value

A data.frame with one row per marker: name, n_f1 (likely F1s genotyped), het_f1 (their share of heterozygotes) and flagged. Attribute n_f1 gives the number of likely F1s; with fewer than about 5, the check says little.

Examples

ex <- hybridclock_example()
mk <- diagnostic_markers(ex$genotypes, ex$groups, "species1", "species2", locus = ex$locus)
chk <- check_markers(ex$genotypes, mk, hybrid_scores(ex$genotypes, mk))
attr(chk, "n_f1")
#> [1] 0