framework_map: Design linkage map framework in two steps: i) estimating the...

In mmollina/MAPPoly: Genetic Linkage Maps in Autopolyploids

Design linkage map framework in two steps: i) estimating the recombination fraction with HMM approach for each parent separately using only markers segregating individually (e.g. map 1 - P1:3 x P2:0, P1: 2x4; map 2 - P1:0 x P2:3, P1:4 x P2:2); ii) merging both maps and re-estimate recombination fractions.

Description

Design linkage map framework in two steps: i) estimating the recombination fraction with HMM approach for each parent separately using only markers segregating individually (e.g. map 1 - P1:3 x P2:0, P1: 2x4; map 2 - P1:0 x P2:3, P1:4 x P2:2); ii) merging both maps and re-estimate recombination fractions.

Usage

framework_map(
  input.seq,
  twopt,
  start.set = 10,
  thres.twopt = 10,
  thres.hmm = 30,
  extend.tail = 30,
  inflation.lim.p1 = 5,
  inflation.lim.p2 = 5,
  phase.number.limit = 10,
  tol = 0.01,
  tol.final = 0.001,
  verbose = TRUE,
  method = "hmm"
)

Arguments

input.seq	object of class mappoly.sequence
twopt	object of class mappoly.twopt
start.set	number of markers to start the phasing procedure (default = 4)
thres.twopt	the LOD threshold used to determine if the linkage phases compared via two-point analysis should be considered for the search space reduction (default = 5)
thres.hmm	the LOD threshold used to determine if the linkage phases compared via hmm analysis should be evaluated in the next round of marker inclusion (default = 50)
extend.tail	the length of the chain's tail that should be used to calculate the likelihood of the map. If NULL (default), the function uses all markers positioned. Even if info.tail = TRUE, it uses at least extend.tail as the tail length
inflation.lim.p1	the maximum accepted length difference between the current and the previous parent 1 sub-map defined by arguments info.tail and extend.tail. If the size exceeds this limit, the marker will not be inserted. If NULL(default), then it will insert all markers.
inflation.lim.p2	same as 'inflation.lim.p1' but for parent 2 sub-map.
phase.number.limit	the maximum number of linkage phases of the sub-maps defined by arguments info.tail and extend.tail. Default is 20. If the size exceeds this limit, the marker will not be inserted. If Inf, then it will insert all markers.
tol	the desired accuracy during the sequential phase of each parental map (default = 10e-02)
tol.final	the desired accuracy for the final parental map (default = 10e-04)
verbose	If TRUE (default), current progress is shown; if FALSE, no output is produced
method	indicates whether to use 'hmm' (Hidden Markov Models), 'ols' (Ordinary Least Squares) to re-estimate the recombination fractions while merging the parental maps (default:hmm)

Value

list containing three mappoly.map objects:1) map built with markers with segregation information from parent 1; 2) map built with markers with segregation information from parent 2; 3) maps in 1 and 2 merged

Author(s)

Marcelo Mollinari, [e-mail] with documentation and minor modifications by Cristiane Taniguti [e-mail]

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