mappoly (version 0.4.1)

calc_genoprob_single_parent: Compute conditional probabilities of the genotype (one informative parent)

Description

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

Usage

calc_genoprob_single_parent(
  input.map,
  step = 0,
  info.parent = 1,
  uninfo.parent = 2,
  global.err = 0,
  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 (with exceptions)

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.

info.parent

index for informative parent

uninfo.parent

index for uninformative parent

global.err

the assumed global error rate (default = 0.0)

phase.config

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

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

 ## tetraploid example
 s <- make_seq_mappoly(tetra.solcap, 'seq12', info.parent = "p1")
 tpt <- est_pairwise_rf(s)
 map <- est_rf_hmm_sequential(input.seq = s,
                              twopt = tpt,
                               start.set = 10,
                               thres.twopt = 10, 
                               thres.hmm = 10,
                               extend.tail = 4,
                               info.tail = TRUE, 
                               sub.map.size.diff.limit = 8, 
                               phase.number.limit = 4,
                               reestimate.single.ph.configuration = TRUE,
                               tol = 10e-2,
                               tol.final = 10e-3)
 plot(map)                                     
 probs <- calc_genoprob_single_parent(input.map = map, 
                                   info.parent = 1, 
                                   uninfo.parent = 2, 
                                   step = 1)
 probs
 ## displaying individual 1, 6 genotypic states
 ## (rows) across linkage group 1 (columns)                          
 image(t(probs$probs[,,2]))