mappoly (version 0.4.1)

paralell_pairwise_probability: 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
)

Value

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

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.