record: Recombination Counting and Ordering
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 Recombination Counting and Ordering (Van Os et al., 2005).

1	record(input.seq, times = 10, LOD = 0, max.rf = 0.5, tol = 1e-04)

`input.seq`	an object of class `sequence`.
`times`	integer. Number of replicates of the RECORD procedure.
`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.

Recombination Counting and Ordering (RECORD) 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.

After determining the order with RECORD, 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.

Marcelo Mollinari, mmollina@usp.br

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.

Van Os, H., Stam, P., Visser, R.G.F. and Van Eck, H.J. (2005) RECORD: a novel method for ordering loci on a genetic linkage map. Theoretical and Applied Genetics 112: 30-40.

make.seq and map

## Not run: 
  ##outcross example
  data(example.out)
  twopt <- rf.2pts(example.out)
  all.mark <- make.seq(twopt,"all")
  groups <- group(all.mark)
  LG1 <- make.seq(groups,1)
  LG1.rec <- record(LG1)

## End(Not run)