mappoly (version 0.4.1)

calc_genoprob_dist: Compute conditional probabilities of the genotypes using probability distribution of dosages

Description

Conditional genotype probabilities are calculated for each marker position and each individual given a map. In this function, the probabilities are not calculated between markers.

Usage

calc_genoprob_dist(
  input.map,
  dat.prob = NULL,
  phase.config = "best",
  verbose = TRUE
)

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

Arguments

input.map

An object of class mappoly.map

dat.prob

an object of class mappoly.data containing the probability distribution of the genotypes

phase.config

which phase configuration should be used. "best" (default) will choose the phase configuration with the maximum likelihood

verbose

if TRUE (default), the current progress is shown; if FALSE, no output is produced

Author

Marcelo Mollinari,

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_. tools:::Rd_expr_doi("10.1534/g3.119.400378")

Examples

 ## tetraploid example
 probs.t <- calc_genoprob_dist(input.map = solcap.prior.map[[1]],
                           dat.prob = tetra.solcap.geno.dist,
                           verbose = TRUE)
 probs.t
 ## displaying individual 1, 36 genotypic states 
 ## (rows) across linkage group 1 (columns)                          
 image(t(probs.t$probs[,,1]))