est_full_hmm_with_global_error: Re-estimate genetic map given a global genotyping error
In mmollina/MAPPoly: Genetic Linkage Maps in Autopolyploids

est_full_hmm_with_global_error

R Documentation

Re-estimate genetic map given a global genotyping error

Description

This function considers a global error when re-estimating a genetic map using Hidden Markov models. Since this function uses the whole transition space in the HMM, its computation can take a while, especially for hexaploid maps.

Usage

est_full_hmm_with_global_error(
  input.map,
  error = NULL,
  tol = 0.001,
  restricted = TRUE,
  th.prob = 0.95,
  verbose = FALSE
)

Arguments

`input.map`	an object of class `mappoly.map`
`error`	the assumed global error rate (default = NULL)
`tol`	the desired accuracy (default = 10e-04)
`restricted`	if `TRUE` (default), restricts the prior to the possible classes under Mendelian, non double-reduced segregation given dosage of the parents
`th.prob`	the threshold for using global error or genotype probability distribution if present in the dataset (default = 0.95)
`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, mmollin@ncsu.edu

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)
    err.submap <- est_full_hmm_with_global_error(submap, 
                                                 error = 0.01, 
                                                 tol = 10e-4, 
                                                 verbose = TRUE)
    err.submap
    plot_map_list(list(dose = submap, err = err.submap), 
                  title = "estimation procedure")

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