Find loci shared by both species — shared

Keeps SNPs that are common in both reference groups and differ little between them. Inbreeding and linkage disequilibrium measured at these loci help separate inbreeding from hybrid age (see sample_summaries()).

Usage

shared_loci(
  geno,
  groups,
  ref1,
  ref2,
  min_maf = 0.05,
  max_diff = 0.1,
  locus = NULL
)

Arguments

geno: Genotype matrix, animals in rows and SNPs in columns, counting copies of one allele (0, 1, 2; NA for missing).
groups: Group label of each animal.
ref1, ref2: Labels of the two reference groups. ref2 defines species 2, whose alleles the hybrid index counts.
min_maf: Smallest minor allele frequency required in each group.
max_diff: Largest allele frequency difference allowed between groups.
locus: Optional locus name of each SNP.

Value

A data.frame with column, name and the pooled allele frequency freq.

Examples

ex <- hybridclock_example()
nrow(shared_loci(ex$genotypes, ex$groups, "species1", "species2", locus = ex$locus))
#> [1] 106