try_seq: Try to map a marker into every possible position between markers in a given map

Description

For a given linkage map, tries do add an additional unpositioned marker. This function estimates parameters for all possible maps including the new marker in all posible positions, while keeping the original linkage map unaltered.

Usage

try_seq(input.seq, mrk, tol = 0.1, pos = NULL, verbose = FALSE)

Arguments

input.seq

an object of class sequence with a predefined order.

mrk

the index of the marker to be tried, according to the input file.

tol

tolerance for the C routine, i.e., the value used to evaluate convergence.

pos

defines in which position the new marker mrk should be placed for the diagnostic graphic. If NULL (default), the marker is placed on the best position i.e. the one which results LOD = 0.00

verbose

if FALSE (default), simplified output is displayed. if TRUE, detailed output is displayed.

Value

An object of class try, which is a list containing the following components:

ord

a list containing results for every linkage map estimated. These results include linkage phases, recombination frequencies and log-likelihoods.

LOD

a vector with LOD-Scores for each position where the additional marker is placed. This Score is based on the best combination of linkage phases for each map.

try.ord

a matrix with the orders of all linkage maps.

data.name

name of the object of class onemap with the raw data.

twopt

name of the object of class rf_2pts with the 2-point analyses.

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 genetic 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

Examples

Run this code

# NOT RUN {
# }
# NOT RUN {
  #outcrossing example
  data(onemap_example_out)
  twopt <- rf_2pts(onemap_example_out)
  markers <- make_seq(twopt,c(2,3,12,14))
  markers.comp <- compare(markers)
  base.map <- make_seq(markers.comp,1)

  extend.map <- try_seq(base.map,30)
  extend.map
  print(extend.map,5) # best position
  print(extend.map,4) # second best position

  #F2 example
  data(mapmaker_example_f2)
  twopt <- rf_2pts(mapmaker_example_f2)
  all_mark <- make_seq(twopt,"all")
  groups <- group(all_mark)
  LG3 <- make_seq(groups,3)
  LG3.ord <- order_seq(LG3, subset.search = "twopt", twopt.alg = "rcd", touchdown=TRUE)
  LG3.ord
  safe.map<-make_seq(LG3.ord,"safe")
  extend.map <- try_seq(safe.map,64)
  extend.map
  (new.map<-make_seq(extend.map,14)) # best position
# }