est_full_hmm_with_prior_prob: Re-estimate genetic map using dosage prior probability...

In mmollina/MAPPoly: Genetic Linkage Maps in Autopolyploids

Re-estimate genetic map using dosage prior probability distribution

Description

This function considers dosage prior distribution when re-estimating a genetic map using Hidden Markov models

Usage

est_full_hmm_with_prior_prob(
  input.map,
  dat.prob = NULL,
  phase.config = "best",
  tol = 0.001,
  verbose = FALSE
)

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 maximum likelihood configuration
tol	the desired accuracy (default = 10e-04)
verbose	if TRUE, current progress is shown; if FALSE (default), no output is produced

Value

A list of class mappoly.map with two elements:

i) info: a list containing information about the map, regardless of the linkage phase configuration:

ploidy	the ploidy level
n.mrk	number of markers
seq.num	a vector containing the (ordered) indices of markers in the map, according to the input file
mrk.names	the names of markers in the map
seq.dose.p1	a vector containing the dosage in parent 1 for all markers in the map
seq.dose.p2	a vector containing the dosage in parent 2 for all markers in the map
chrom	a vector indicating the sequence (usually chromosome) each marker belongs as informed in the input file. If not available, chrom = NULL
genome.pos	physical position (usually in megabase) of the markers into the sequence
seq.ref	reference base used for each marker (i.e. A, T, C, G). If not available, seq.ref = NULL
seq.alt	alternative base used for each marker (i.e. A, T, C, G). If not available, seq.ref = NULL
chisq.pval	a vector containing p-values of the chi-squared test of Mendelian segregation for all markers in the map
data.name	name of the dataset of class mappoly.data
ph.thres	the LOD threshold used to define the linkage phase configurations to test

ii) a list of maps with possible linkage phase configuration. Each map in the list is also a list containing

seq.num	a vector containing the (ordered) indices of markers in the map, according to the input file
seq.rf	a vector of size (n.mrk - 1) containing a sequence of recombination fraction between the adjacent markers in the map
seq.ph	linkage phase configuration for all markers in both parents
loglike	the hmm-based multipoint likelihood

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_. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1534/g3.119.400378")}

Examples

    submap <- get_submap(solcap.dose.map[[1]], mrk.pos = 1:20, verbose = FALSE)
    prob.submap <- est_full_hmm_with_prior_prob(submap,
                                                dat.prob = tetra.solcap.geno.dist,
                                                tol = 10e-4, 
                                                verbose = TRUE)
    prob.submap
    plot_map_list(list(dose = submap, prob = prob.submap), 
                  title = "estimation procedure")

mmollina/MAPPoly documentation built on March 8, 2024, 2:04 a.m.