Find diagnostic markers between two reference groups — diagnostic

Keeps SNPs that are nearly fixed for different alleles in two reference groups of (presumed) pure animals: at most threshold frequency in one group and at least 1 - threshold in the other. With locus, only the first such SNP per locus is kept, so markers are effectively unlinked.

Usage

diagnostic_markers(geno, groups, ref1, ref2, threshold = 0.01, 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.
threshold: Largest frequency allowed for the minor allele in each reference group (0.01 keeps markers within 1% of fixation).
locus: Optional locus name of each SNP.

Value

A data.frame with one row per marker: column (index in geno), name, flip (TRUE when the counted allele belongs to species 1), and the counted allele's frequency in each reference group (freq1, freq2).

Examples

ex <- hybridclock_example()
mk <- diagnostic_markers(ex$genotypes, ex$groups, "species1", "species2", locus = ex$locus)
nrow(mk)
#> [1] 314