update_framework_map: Add markers that are informative in both parents using HMM...

In mmollina/MAPPoly: Genetic Linkage Maps in Autopolyploids

Add markers that are informative in both parents using HMM approach and evaluating difference in LOD and gap size

Description

Add markers that are informative in both parents using HMM approach and evaluating difference in LOD and gap size

Usage

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
)

Arguments

input.map.list	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
input.seq	object of class mappoly.sequence containing all markers for specific group
twopt	object of class mappoly.twopt
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)
init.LOD	the LOD threshold used to determine if the marker will be included or not after hmm analysis (default = 30)
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) or 'wMDS_to_1D_pc' (weighted MDS followed by fitting a one dimensional principal curve) to re-estimate the recombination fractions after adding markers
input.mds	An object of class mappoly.map
max.rounds	integer defining number of times to try to fit the remaining markers in the sequence
size.rem.cluster	threshold for number of markers that must contain in a segment after a gap is removed to keep this segment in the sequence
gap.threshold	threshold for gap size

Value

object of class mappoly.map2

Author(s)

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

mmollina/MAPPoly documentation built on March 8, 2024, 2:04 a.m.