mappoly (version 0.4.1)

add_md_markers: 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

Marcelo Mollinari, with documentation and minor modifications by Cristiane Taniguti