calc_genoprob: Compute conditional probabilities of the genotypes

In mappoly: Genetic Linkage Maps in Autopolyploids

Compute conditional probabilities of the genotypes

Description

Conditional genotype probabilities are calculated for each marker position and each individual given a map.

Usage

calc_genoprob(input.map, step = 0, phase.config = "best", verbose = TRUE)

Arguments

input.map	An object of class mappoly.map
step	Maximum distance (in cM) between positions at which the genotype probabilities are calculated, though for step = 0, probabilities are calculated only at the marker locations.
phase.config	which phase configuration should be used. "best" (default) will choose the phase configuration associated with the maximum likelihood
verbose	if TRUE (default), current progress is shown; if FALSE, no output is produced

Value

An object of class 'mappoly.genoprob' which has two elements: a tridimensional array containing the probabilities of all possible genotypes for each individual in each marker position; and the marker sequence with it's recombination frequencies

Author(s)

Marcelo Mollinari, [e-mail]

References

Mollinari, M., and Garcia, A. A. F. (2019) Linkage analysis and haplotype phasing in experimental autopolyploid populations with high ploidy level using hidden Markov models, _G3: Genes, Genomes, Genetics_. doi: 10.1534/g3.119.400378

Examples

 ## tetraploid example
 probs.t <- calc_genoprob(input.map = solcap.dose.map[[1]],
                        verbose = TRUE)
 probs.t
 ## displaying individual 1, 36 genotypic states
 ## (rows) across linkage group 1 (columns)                          
 image(t(probs.t$probs[,,1]))

mappoly documentation built on Jan. 6, 2023, 1:16 a.m.