p4_functions: Calculate recombination frequency, LOD and log-likelihood from frequency tables in a preferential pairing tetraploid

Description

This group of functions is called by linkage.

Usage

p4_1.0_1.0(x, p1, p2, ncores = 1)
p4_1.0_1.1(x, p1, p2, ncores = 1)
p4_1.0_1.2(x, p1, p2, ncores = 1)
p4_1.0_1.3(x, p1, p2, ncores = 1)
p4_1.0_2.0(x, p1, p2, ncores = 1)
p4_1.0_2.1(x, p1, p2, ncores = 1)
p4_1.0_2.2(x, p1, p2, ncores = 1)
p4_1.1_1.1(x, p1, p2, ncores = 1)
p4_1.1_1.2(x, p1, p2, ncores = 1)
p4_1.1_1.3(x, p1, p2, ncores = 1)
p4_1.1_2.2(x, p1, p2, ncores = 1)
p4_1.2_1.2(x, p1, p2, ncores = 1)
p4_1.2_2.1(x, p1, p2, ncores = 1)
p4_1.2_2.2(x, p1, p2, ncores = 1)
p4_1.3_1.2(x, p1, p2, ncores = 1)
p4_1.3_1.3(x, p1, p2, ncores = 1)
p4_1.3_2.1(x, p1, p2, ncores = 1)
p4_1.3_2.2(x, p1, p2, ncores = 1)
p4_2.0_1.1(x, p1, p2, ncores = 1)
p4_2.0_1.2(x, p1, p2, ncores = 1)
p4_2.0_1.3(x, p1, p2, ncores = 1)
p4_2.0_2.0(x, p1, p2, ncores = 1)
p4_2.0_2.1(x, p1, p2, ncores = 1)
p4_2.0_2.2(x, p1, p2, ncores = 1)
p4_2.1_2.2(x, p1, p2, ncores = 1)
p4_2.2_2.2(x, p1, p2, ncores = 1)

Arguments

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.

Preferential pairing parameter for parent 1, numeric value in range 0 <= p1 < 2/3

Preferential pairing parameter for parent 2, numeric value in range 0 <= p2 < 2/3

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.