framework_map: Design linkage map framework in two steps: i) estimating the...
In mappoly: Genetic Linkage Maps in Autopolyploids

framework_map

R Documentation

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