rcd: Rapid Chain Delineation
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 Rapid Chain Delineation (Doerge, 1996).

1	rcd(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.

Rapid Chain Delineation (RCD) 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. Next is an excerpt from QTL Cartographer Version 1.17 Manual describing the RCD algorithm (Basten et al., 2005):

The linkage group is initiated with the pair of markers having the smallest recombination fraction. The remaining markers are placed in a “pool” awaiting placement on the map. The linkage group is extended by adding markers from the pool of unlinked markers. Each terminal marker of the linkage group is a candidate for extension of the chain: The unlinked marker that has the smallest recombination fraction with either is added to the chain subject to the provision that the recombination fraction is statistically significant at a prespecified level. This process is repeated as long as markers can be added to the chain.

After determining the order with RCD, 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

Basten, C. J., Weir, B. S. and Zeng, Z.-B. (2005) QTL Cartographer Version 1.17: A Reference Manual and Tutorial for QTL Mapping.

Doerge, R. W. (1996) Constructing genetic maps by rapid chain delineation. Journal of Quantitative Trait Loci 2: 121-132.

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)
  LG1 <- make.seq(groups,1)
  LG1.rcd <- rcd(LG1)

## End(Not run)