ripple.seq: Compares and displays plausible alternative orders for a...
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

For a given sequence of ordered markers, computes the multipoint likelihood of alternative orders, by shuffling subsets (windows) of markers within the sequence. For each position of the window, all possible (ws)! orders are compared.

1	ripple.seq(input.seq, ws = 4, LOD = 3, tol = 0.1)

`input.seq`	an object of class `sequence` with a predefined order.
`ws`	an integer specifying the length of the window size (defaults to 4).
`LOD`	threshold for the LOD-Score, so that alternative orders with LOD less then or equal to this threshold will be displayed.
`tol`	tolerance for the C routine, i.e., the value used to evaluate convergence.

Large values for the window size make computations very slow, specially if there are many partially informative markers.

This function does not return any value; it just produces text output to suggest alternative orders.

Gabriel R A Margarido, gramarga@gmail.com and Marcelo Mollinari, mmollina@usp.br

Broman, K. W., Wu, H., Churchill, G., Sen, S., Yandell, B. (2008) qtl: Tools for analyzing QTL experiments R package version 1.09-43

Jiang, C. and Zeng, Z.-B. (1997). Mapping quantitative trait loci with dominant and missing markers in various crosses from two inbred lines. Genetica 101: 47-58.

Lander, E. S., Green, P., Abrahamson, J., Barlow, A., Daly, M. J., Lincoln, S. E. and Newburg, L. (1987) MAPMAKER: An interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1: 174-181.

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.

Wu, R., Ma, C.-X., Painter, I. and Zeng, Z.-B. (2002a) Simultaneous maximum likelihood estimation of linkage and linkage phases in outcrossing species. Theoretical Population Biology 61: 349-363.

Wu, R., Ma, C.-X., Wu, S. S. and Zeng, Z.-B. (2002b). Linkage mapping of sex-specific differences. Genetical Research 79: 85-96

make.seq, compare, try.seq and order.seq.

## Not run: 
 #Outcross example
  data(example.out)
  twopt <- rf.2pts(example.out)
  markers <- make.seq(twopt,c(27,16,20,4,19,21,23,9,24,29))
  markers.map <- map(markers)
  ripple.seq(markers.map)

## End(Not run)