seriation: Seriation
In bschiffthaler/BatchMap: Software for the Creation of High Density Linkage Maps in Outcrossing Species

Description Usage Arguments Details Value Author(s) References See Also Examples

Implements the marker ordering algorithm Seriation (Buetow & Chakravarti, 1987).

1	seriation(input.seq, LOD = 0, max.rf = 0.5, tol = 1e-04)

`input.seq`	an object of class `sequence`.
`LOD`	minimum LOD-Score threshold used when constructing the pairwise recombination fraction matrix.
`max.rf`	maximum recombination fraction threshold used as the LOD value above.
`tol`	tolerance for the C routine, i.e., the value used to evaluate convergence.

Seriation is an algorithm for marker ordering in linkage groups. It is not an exhaustive search method and, therefore, is not computationally intensive. However, it does not guarantee that the best order is always found. The only requirement is a matrix with recombination fractions between markers.

NOTE: When there are to many pairs of markers with the same value in the recombination fraction matrix, it can result in ties during the ordination process and the Seriation algorithm may not work properly. This is particularly relevant for outcrossing populations with mixture of markers of type D1 and D2. When this occurs, the function shows the following error message: There are too many ties in the ordination process - please, consider using another ordering algorithm.

After determining the order with Seriation, the final map is constructed using the multipoint approach (function map).

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 `outcross` with the raw data.
`twopt`	name of the object of class `rf.2pts` with the 2-point analyses.

Gabriel R A Margarido, gramarga@gmail.com

Buetow, K. H. and Chakravarti, A. (1987) Multipoint gene mapping using seriation. I. General methods. American Journal of Human Genetics 41: 180-188.

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.

make.seq, map

## Not run: 
  ##outcross example
  data(example.out)
  twopt <- rf.2pts(example.out)
  all.mark <- make.seq(twopt,"all")
  groups <- group(all.mark)
  LG3 <- make.seq(groups,3)
  LG3.ser <- seriation(LG3)

## End(Not run)