get_submap: Extract sub-map from map

In mmollina/MAPpoly: Genetic Linkage Maps in Autopolyploids

Extract sub-map from map

Description

Given a pre-constructed map, it extracts a sub-map for a provided sequence of marker positions. Optionally, it can update the linkage phase configurations and respective recombination fractions.

Usage

get_submap(
  input.map,
  mrk.pos,
  phase.config = "best",
  reestimate.rf = TRUE,
  reestimate.phase = FALSE,
  thres.twopt = 5,
  thres.hmm = 3,
  extend.tail = 50,
  tol = 0.1,
  tol.final = 0.001,
  use.high.precision = FALSE,
  verbose = TRUE
)

Arguments

input.map	An object of class mappoly.map
mrk.pos	positions of the markers that should be considered in the new map. This can be in any order
phase.config	which phase configuration should be used. "best" (default) will choose the configuration associated with the maximum likelihood
reestimate.rf	logical. If TRUE (default) the recombination fractions between markers are re-estimated
reestimate.phase	logical. If TRUE, the linkage phase configurations are re-estimated (default = FALSE)
thres.twopt	the LOD threshold used to determine if the linkage phases compared via two-point analysis should be considered (default = 5)
thres.hmm	the threshold used to determine if the linkage phases compared via hmm analysis should be considered (default = 3)
extend.tail	the length of the tail of the chain that should be used to calculate the likelihood of the linkage phases. If info.tail = TRUE, the function uses at least extend.tail as the length of the tail (default = 50)
tol	the desired accuracy during the sequential phase (default = 0.1)
tol.final	the desired accuracy for the final map (default = 10e-04)
use.high.precision	logical. If TRUE uses high precision (long double) numbers in the HMM procedure implemented in C++, which can take a long time to perform (default = FALSE)
verbose	If TRUE (default), current progress is shown; if FALSE, no output is produced

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

 
    ## selecting the six first markers in linkage group 1
    ## re-estimating the recombination fractions and linkage phases
    submap1.lg1 <- get_submap(input.map = maps.hexafake[[1]], 
                           mrk.pos = 1:6, verbose = TRUE,
                           reestimate.phase = TRUE,  
                           tol.final = 10e-3)
   ## no recombination fraction re-estimation: first 20 markers
   submap2.lg1 <- get_submap(input.map = maps.hexafake[[1]], 
                           mrk.pos = 1:20, reestimate.rf = FALSE,
                           verbose = TRUE, 
                           tol.final = 10e-3)
  plot(maps.hexafake[[1]])
  plot(submap1.lg1, mrk.names = TRUE, cex = .8)
  plot(submap2.lg1, mrk.names = TRUE, cex = .8)
  

mmollina/MAPpoly documentation built on March 9, 2024, 2:52 a.m.