mappoly (version 0.4.1)

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,
  size.rem.cluster = 1,
  phase.config = "best",
  thres.twopt = 3,
  thres.hmm = "best",
  tol.merge = 0.001,
  tol.final = 0.001,
  verbose = TRUE
)

Value

An object of class mappoly.map

Arguments

input.map

an object of class mappoly.map

twopt

an object of class mappoly.twopt 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

size.rem.cluster

the size of the marker cluster (in number of markers) from which the cluster should be removed. The default value is 1

phase.config

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

thres.twopt

the threshold used to determine if the linkage phases compared via two-point analysis should be considered for the search space reduction (default = 3)

thres.hmm

the threshold used to determine which linkage phase configurations should be returned when merging two maps. If "best" (default), returns only the best linkage phase configuration. NOTE: if merging multiple maps, it always uses the "best" linkage phase configuration at each block insertion.

tol.merge

the desired accuracy for merging maps (default = 10e-04)

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

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

 map <- get_submap(solcap.dose.map[[1]], 1:20, verbose = FALSE)
 tpt <- est_pairwise_rf(make_seq_mappoly(map))
 new.map <- split_and_rephase(map, tpt, 1, 1)
 map
 new.map
 plot_map_list(list(old.map = map, new.map = new.map), col = "ggstyle")