onemap (version 3.0.0)

ripple_seq: Compares and displays plausible alternative orders for a given linkage group

Description

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.

Usage

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

Value

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

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.

Author

Gabriel R A Margarido, and Marcelo Mollinari,

Details

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

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.

Examples

# \donttest{
#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)
# }