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Add markers to a pre-existing sequence using HMM analysis and evaluating difference in LOD
add_md_markers(
input.map,
mrk.to.include,
input.seq,
input.matrix,
input.genoprob,
input.data,
input.mds = NULL,
thresh = 500,
extend.tail = 50,
method = c("hmm", "wMDS_to_1D_pc"),
verbose = TRUE
)An object of class mappoly.map
vector for marker names to be included
an object of class mappoly.sequence containing all markers (the ones in the mappoly.map and also the ones to be included)
object of class mappoly.rf.matrix
an object of class mappoly.genoprob obtained with calc_genoprob of the input.map object
an object of class mappoly.data
An object of class mappoly.map
the LOD threshold used to determine if the marker will be included or not after hmm analysis (default = 30)
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
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
If TRUE (default), current progress is shown; if FALSE, no output is produced
Marcelo Mollinari, mmollin@ncsu.edu with documentation and minor modifications by Cristiane Taniguti chtaniguti@tamu.edu