Add markers that are informative in both parents using HMM approach and evaluating difference in LOD and gap size
update_framework_map(
input.map.list,
input.seq,
twopt,
thres.twopt = 10,
init.LOD = 30,
verbose = TRUE,
method = "hmm",
input.mds = NULL,
max.rounds = 50,
size.rem.cluster = 2,
gap.threshold = 4
)object of class mappoly.map2
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 containing all markers for specific group
object of class mappoly.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)
the LOD threshold used to determine if the marker will be included or not after hmm analysis (default = 30)
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) or 'wMDS_to_1D_pc' (weighted MDS followed by fitting a one dimensional principal curve) to re-estimate the recombination fractions after adding markers
An object of class mappoly.map
integer defining number of times to try to fit the remaining markers in the sequence
threshold for number of markers that must contain in a segment after a gap is removed to keep this segment in the sequence
threshold for gap size
Marcelo Mollinari, mmollin@ncsu.edu with documentation and minor modifications by Cristiane Taniguti chtaniguti@tamu.edu