r3_functions: Calculate recombination frequency, LOD and log-likelihood...

In polymapR: Linkage Analysis in Outcrossing Polyploids

Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing triploid from a tetraploid x diploid cross.

Description

This group of functions is called by linkage.

Usage

r3_0.1_0.1(x, ncores = 1)

r3_0.1_1.1(x, ncores = 1)

r3_0.1_2.1(x, ncores = 1)

r3_2.1_2.1(x, ncores = 1)

Arguments

x	A frequency table of the different classes of dosages in the progeny. The column names start with "n_". Followed by the dosage of the first marker and then of the second.
ncores	Number of cores to use for parallel processing (deprecated).

Value

A list with the following items:

r_mat	A matrix with recombination frequencies for the different phases
LOD_mat	A matrix with LOD scores for the different phases
logL_mat	A matrix with log likelihood ratios for the different phases
phasing_strategy	A character string specifying the phasing strategy. "MLL" for maximum likelihood en "MINR" for minimum recombination frequency.
possible_phases	The phases between markers that are possible. Same order and length as column names of output matrices.

polymapR documentation built on Nov. 5, 2023, 1:09 a.m.