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.
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"
)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
object of class mappoly.sequence
object of class mappoly.twopt
number of markers to start the phasing procedure (default = 4)
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)
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)
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
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.
same as `inflation.lim.p1` but for parent 2 sub-map.
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.
the desired accuracy during the sequential phase of each parental map (default = 10e-02)
the desired accuracy for the final parental map (default = 10e-04)
If TRUE (default), current progress is shown; if FALSE, no output is produced
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)
Marcelo Mollinari, mmollin@ncsu.edu with documentation and minor modifications by Cristiane Taniguti chtaniguti@tamu.edu