MDSMap:High density linkage maps using multi-dimensional scaling

We present an R-package MDSMap, which contains functions relevant to robust methods for rapid construction of high density linkage maps suitable for a variety of experimental genetic populations from homozygous or heterozygous parents in diploids or autotetraploids. The approach uses multi-dimensional scaling to order markers within a linkage group using pairwise recombination fractions (or mappings thereof) weighted by LOD scores (logarithm10 of the odds ratio). Functions are included to allow evaluation adjustment of the estimated order and comparison to some external “truth”. The estimation is a two step process using unconstrained SMACOF followed by either spherically constrained SMACOF or fitting a principal curve using the R-packages smacof and princurve.