mappoly (version 0.4.1)

calc_genoprob_error: 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
)

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

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

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

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