ripple_seq function

Compares and displays plausible alternative orders for a given linkage group

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.

ripple_seq(input.seq, ws = 4, ext.w = NULL, LOD = 3, tol = 0.1, verbose = TRUE)

Arguments

• input.seq: an object of class sequence with a predefined order.
• ws: an integer specifying the length of the window size (defaults to 4).
• ext.w: an integer specifying how many markers should be considered in the vicinity of the permuted window. If ext.w=NULL all markers in the sequence are considered. In this version, it is used only in backcross, $F_2$ or RIL crosses.
• 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.
• verbose: A logical, if TRUE it output progress status information.

Returns

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

Details

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

Examples

#Outcross example
 data(onemap_example_out)
 twopt <- rf_2pts(onemap_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)

#F2 example
data(onemap_example_f2)
twopt <- rf_2pts(onemap_example_f2)
all_mark <- make_seq(twopt,"all")
groups <- group(all_mark)
LG3 <- make_seq(groups,1)
LG3.ord <- order_seq(LG3, subset.search = "twopt", twopt.alg = "rcd", touchdown=TRUE)
LG3.ord
make_seq(LG3.ord) # get safe sequence
ord.1<-make_seq(LG3.ord,"force") # get forced sequence
ripple_seq(ord.1, ws=5)

References

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

See Also

make_seq, compare, try_seq

and order_seq.

Author(s)

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