mds_onemap: OneMap interface with MDSMap package with option for multipoint distances estimation

Description

For a given sequence of markers, apply mds method described in Preedy and Hackett (2016) using MDSMap package to ordering markers and estimates the genetic distances with OneMap multipoint approach. Also gives MDSMap input file format for directly analysis in this package.

Usage

mds_onemap(
  input.seq,
  out.file = NULL,
  p = NULL,
  ispc = TRUE,
  displaytext = FALSE,
  weightfn = "lod2",
  mapfn = "haldane",
  ndim = 2,
  rm_unlinked = TRUE,
  size = NULL,
  overlap = NULL,
  phase_cores = 1,
  tol = 1e-05,
  hmm = TRUE,
  parallelization.type = "PSOCK"
)

Value

An object of class sequence, which is a list containing the following components:

seq.num: a vector containing the (ordered) indices of markers in the sequence, according to the input file.
seq.phases: a vector with the linkage phases between markers in the sequence, in corresponding positions. -1 means that there are no defined linkage phases.
seq.rf: a vector with the recombination frequencies between markers in the sequence. -1 means that there are no estimated recombination frequencies.
seq.like: log-likelihood of the corresponding linkage map.
data.name: name of the object of class onemap with the raw data.
twopt: name of the object of class rf_2pts with the 2-point analyses.

Arguments

input.seq: an object of class sequence
out.file: path to the generated MDSMap input file.
p: Integer - the penalty for deviations from the sphere - higher p forces points more closely onto a sphere.
ispc: Logical determining the method to be used to estimate the map. By default this is TRUE and the method of principal curves will be used. If FALSE then the constrained MDS method will be used.
displaytext: Shows markers names in analysis graphic view
weightfn: Character string specifying the values to use for the weight matrix in the MDS 'lod2' or 'lod'.
mapfn: Character string specifying the map function to use on the recombination fractions 'haldane' is default, 'kosambi' or 'none'.
ndim: number of dimensions to be considered in the multidimensional scaling procedure (default = 2)
rm_unlinked: When some pair of markers do not follow the linkage criteria, if TRUE one of the markers is removed and mds is performed again.
size: The center size around which an optimum is to be searched
overlap: The desired overlap between batches
phase_cores: The number of parallel processes to use when estimating the phase of a marker. (Should be no more than 4)
tol: tolerance for the C routine, i.e., the value used to evaluate convergence.
hmm: logical defining if the HMM must be applied to estimate multipoint genetic distances
parallelization.type: one of the supported cluster types. This should be either PSOCK (default) or FORK.

Author

Cristiane Taniguti, chtaniguti@tamu.edu

Details

For better description about MDS method, see MDSMap package vignette.

References

Preedy, K. F. and Hackett, C. A. (2016). A rapid marker ordering approach for high-density genetic linkage maps in experimental autotetraploid populations using multidimensional scaling. Theoretical and Applied Genetics 129: 2117-2132

Mollinari, M., Margarido, G. R. A., Vencovsky, R. and Garcia, A. A. F. (2009) Evaluation of algorithms used to order markers on genetics maps. Heredity 103: 494-502.

Wu, R., Ma, C.-X., Painter, I. and Zeng, Z.-B. (2002a) Simultaneous maximum likelihood estimation of linkage and linkage phases in outcrossing species. Theoretical Population Biology 61: 349-363.

Wu, R., Ma, C.-X., Wu, S. S. and Zeng, Z.-B. (2002b). Linkage mapping of sex-specific differences. Genetical Research 79: 85-96