paralell_pairwise_probability: Parallel Pairwise Probability Estimation

In mmollina/MAPpoly: Genetic Linkage Maps in Autopolyploids

Parallel Pairwise Probability Estimation

Description

This function performs parallel pairwise estimation of recombination fractions using probability-based dosage scoring via a C++ backend.

Usage

paralell_pairwise_probability(
  mrk.pairs,
  input.seq,
  geno,
  dP,
  dQ,
  count.cache,
  tol = .Machine$double.eps^0.25,
  ll = ll
)

Arguments

mrk.pairs	A matrix of dimensions 2*N, containing N pairs of markers to be analyzed.
input.seq	An object of class mappoly.sequence.
geno	Genotype matrix.
dP	Vector of probabilities for the first allele.
dQ	Vector of probabilities for the second allele.
count.cache	An object of class cache.info containing pre-computed genotype frequencies.
tol	The tolerance level for the estimation accuracy (default is .Machine$double.eps^0.25).
ll	Logical; if TRUE, the function returns log-likelihood values instead of LOD scores. For internal use.

Value

Depending on the ll parameter, returns either log-likelihood values or formatted LOD scores from pairwise recombination fraction estimation.

mmollina/MAPpoly documentation built on March 9, 2024, 2:52 a.m.