mappoly (version 0.2.3)

split_and_rephase: Divides map in sub-maps and re-phase them

Description

The function splits the input map in sub-maps given a distance threshold of neighboring markers and evaluates alternative phases between the sub-maps.

Usage

split_and_rephase(
  input.map,
  twopt,
  gap.threshold = 5,
  remove.single = TRUE,
  phase.config = "best",
  tol.final = 0.001,
  verbose = TRUE
)

Arguments

input.map

an object of class mappoly.map

twopt

an object of class poly.est.two.pts.pairwise containing the two-point information for the markers contained in input.map

gap.threshold

distance threshold of neighboring markers where the map should be spitted. The default value is 5 cM

remove.single

Should isolated markers be removed?

phase.config

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

tol.final

the desired accuracy for the final map (default = 10e-04)

verbose

if TRUE (default), the current progress is shown; if FALSE, no output is produced

Value

An object of class mappoly.map

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_. 10.1534/g3.119.400378

Examples

# NOT RUN {
 map <- get_submap(maps.hexafake[[1]], 1:20, reestimate.rf = FALSE, reestimate.phase = FALSE)
 tpt <- est_pairwise_rf(make_seq_mappoly(map))
 new.map <- split_and_rephase(map, tpt, 5)
 map
 new.map
 plot_map_list(list(old.map = map, new.map = new.map))

# }