calc_genoprob_error {mappoly}

Compute conditional probabilities of the genotypes using global error

Description

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

Usage

calc_genoprob_error(
  input.map,
  step = 0,
  phase.config = "best",
  error = 0.01,
  th.prob = 0.95,
  restricted = TRUE,
  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 maximum likelihood configuration

error

the assumed global error rate (default = 0.01)

th.prob

the threshold for using global error or genotype probability distribution contained in the dataset (default = 0.95)

restricted

if TRUE (default), restricts the prior to the possible classes under Mendelian non double-reduced segregation given the parental dosages

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

 
     probs.error <- calc_genoprob_error(input.map = solcap.err.map[[1]],
                                error = 0.05,
                                verbose = TRUE)