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

In mmollina/MAPPoly: Genetic Linkage Maps in Autopolyploids

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
)

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

Value

An object of class mappoly.map

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_. \Sexpr[results=rd]{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")

mmollina/MAPPoly documentation built on March 8, 2024, 2:04 a.m.