mds_onemap: OneMap interface with MDSMap package with possibilitie of 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 = "out.file",
  mds.graph.file = "NULL.pdf", p = NULL, n = NULL, ispc = TRUE,
  displaytext = FALSE, weightfn = "lod2", mapfn = "haldane",
  hmm = TRUE, mds.seq = TRUE)

Arguments

input.seq

an object of class sequence

out.file

path to the generated MDSMap input file.

mds.graph.file

path to the graphic generated by MDSMap

Integer - the penalty for deviations from the sphere - higher p forces points more closely onto a sphere.

Vector of integers or strings containing markers to be omitted from the analysis.

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'.

hmm

Multipoint genetic distance estimation

mds.seq

When some pair of markers do not follow the linkage criteria, if TRUE one of the markers is removed and mds is performed again.

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.

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.