onemap (version 0.1-1)

rcd: Rapid Chain Delineation

Description

Implements the marker ordering algorithm Rapid Chain Delineation (Doerge, 1996).

Usage

rcd(r)

Arguments

r

A (symmetric) matrix containing the results of two-point analyses, i.e., pairwise recombination fractions between genetic markers.

Value

• A vector with the estimated order of markers on the linkage group. Numbers are based on the position of each marker on the recombination fraction matrix given as input, i.e., on the row/column each marker occupies on that matrix. No names are displayed (for portability purposes).

Details

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 describring 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.

References

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.

See Also

map, print.map

Examples

rcmb <- c(NA,0.10,0.05,0.10,NA,0.06,0.05,0.06,NA)
  rcmb_mat <- matrix(rcmb,nrow=3,ncol=3,byrow=TRUE) # hypothetical recombination fraction matrix
  colnames(rcmb_mat) <- rownames(rcmb_mat) <- paste("M",1:3,sep="")
  rcmb_mat # not monotonic

  order <- rcd(rcmb_mat)
  order
  
  rcmb_mat[order,order] # monotonic