mappoly (version 0.4.1)

get_submap: 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

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

 # \donttest{
    ## 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)
  # }