View source: R/split_and_rephase.R
split_and_rephase | R Documentation |
The function splits the input map in sub-maps given a distance threshold of neighboring markers and evaluates alternative phases between the sub-maps.
split_and_rephase( input.map, twopt, gap.threshold = 5, size.rem.cluster = 1, phase.config = "best", tol.final = 0.001, verbose = TRUE )
input.map |
an object of class |
twopt |
an object of class |
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 |
tol.final |
the desired accuracy for the final map (default = 10e-04) |
verbose |
if |
An object of class mappoly.map
Marcelo Mollinari, mmollin@ncsu.edu
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_. doi: 10.1534/g3.119.400378
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")
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