r6_functions: Calculate recombination frequency, LOD and log-likelihood...

Description Usage Arguments Value

Description

This group of functions is called by linkage.

Usage

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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.

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.


mdavy86/polymapR documentation built on May 25, 2019, 9:35 p.m.