add_md_markers: Add markers to a pre-existing sequence using HMM analysis and...

In mmollina/MAPpoly: Genetic Linkage Maps in Autopolyploids

Add markers to a pre-existing sequence using HMM analysis and evaluating difference in LOD

Description

Add markers to a pre-existing sequence using HMM analysis and evaluating difference in LOD

Usage

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
)

Arguments

input.map	An object of class mappoly.map
mrk.to.include	vector for marker names to be included
input.seq	an object of class mappoly.sequence containing all markers (the ones in the mappoly.map and also the ones to be included)
input.matrix	object of class mappoly.rf.matrix
input.genoprob	an object of class mappoly.genoprob obtained with calc_genoprob of the input.map object
input.data	an object of class mappoly.data
input.mds	An object of class mappoly.map
thresh	the LOD threshold used to determine if the marker will be included or not after hmm analysis (default = 30)
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
method	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
verbose	If TRUE (default), current progress is shown; if FALSE, no output is produced

Author(s)

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

mmollina/MAPpoly documentation built on March 9, 2024, 2:52 a.m.