Gene-drop true linked genotypes for the two focal individuals in a pedigree

linked_gene_drop_true_genotypes(
  kid,
  pa,
  ma,
  n_alleles,
  map_pos,
  chrom_id,
  chrom_start,
  chrom_end,
  freqs,
  reps,
  min_crossovers = 0L
)

Arguments

kid: integer vector of pedigree IDs.
pa: integer vector of paternal IDs, with 0 for founders.
ma: integer vector of maternal IDs, with 0 for founders.
n_alleles: integer vector with the number of alleles at each locus.
map_pos: numeric vector of map positions in centiMorgans.
chrom_id: integer chromosome ID per locus.
chrom_start: one-based start locus index for each chromosome.
chrom_end: one-based end locus index for each chromosome.
freqs: list of allele-frequency vectors, one per locus.
reps: number of replicate gene drops.
min_crossovers: minimum number of crossovers in the typed marker span of each chromosome for each meiosis.

Value

A list with integer matrices indiv1 and indiv2.