try.seq: Try to map a marker into every possible position between...
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 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.

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

`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.

The diagnostic graphic is made of three figures: i) the top figure represents the new genetic map obtained with the insertion of the new marker mrk on position pos. If pos = NULL (default), the marker is placed on the best position i.e. the one which results LOD = 0.00, which is indicated by a red triangle; ii) the left bottom figure represents the base map (contained in input.seq) on x-axis and the LOD-Scores of the linkage maps obtained with the new marker mrk tested at the beginning, between and at the end of the base map. Actually, it is a graphic representation of the LOD vector (see Value section). The red triangle indicates the best position where the new marker mrk should be placed; iii) the right bottom figure is the non-interactive rf.graph.table function for the new genetic map (deprecated in BatchMap). It plots a matrix of pairwise recombination fractions (under the diagonal) and LOD Scores (upper the diagonal) using a color scale.

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 `outcross` with the raw data.
`twopt`	name of the object of class `rf.2pts` with the 2-point analyses.

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 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

make.seq and compare.

## Not run: 
  #outcrossing example
  data(example.out)
  twopt <- rf.2pts(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


## End(Not run)