probabilities-class: Identity-by-descent genotype probabilities

In mpMap2: Genetic Analysis of Multi-Parent Recombinant Inbred Lines

Description

Identity-by-descent genotype probabilities

Arguments

data	An integer matrix containing the IBD genotype probabilities. Rows correspond to combinations of genetic lines and founder lines, and columns correspond to genetic positions.
key	A matrix identifying how pairs of founder alleles are mapped to rows of the data slot.
map	The map of positions at which IBD genotype probabilities are computed.

Details

This object contains the identify-by-descent genotype probabilities, as computed by computeGenotypeProbabilities. The slot data is a numeric matrix containing the actual computations, where columns correspond to genetic positions.

Describing the rows of the data matrix is more complicated. The slot key is a matrix containing three columns, the first two being founder alleles, and the third being an encoding of that combination. If k is the number of rows in key, then the first k rows of the data matrix correspond to the first genetic line in the population. Specifically, the first row corresponds to genotype probabilities for the first line, for the combination of founder alleles encoding as 1. The second corresponds to genotype probabilities for the first line, for the combination encoded as 2, etc.

mpMap2 documentation built on Sept. 13, 2020, 5:17 p.m.