r3_functions {polymapR}

Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing triploid from a 4x2 or 2x4 cross.

Description

This group of functions is called by linkage.

Usage

r3_2_1.0_1.0(x, ncores = 1)

r3_2_1.0_1.1(x, ncores = 1)

r3_2_1.0_1.2(x, ncores = 1)

r3_2_1.2_1.2(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.