compare: Compare all possible orders (exhaustive search) for a given...
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 with n markers, computes the multipoint likelihood of all n!/2 possible orders.

1	compare(input.seq, n.best = 50, tol = 0.001, verbose = FALSE)

`input.seq`	an object of class `sequence`.
`n.best`	the number of best orders to store in object (defaults to 50).
`tol`	tolerance for the C routine, i.e., the value used to evaluate convergence.
`verbose`	if `FALSE` (default), simplified output is displayed. if `TRUE`, detailed output is displayed.

Since the number n!/2 is large even for moderate values of n, this function is to be used only for sequences with relatively few markers. If markers were genotyped in an outcross population, linkage phases need to be estimated and therefore more states need to be visited in the Markov chain; when segregation types are D1, D2 and C, computation can required a very long time (specially when markers linked in repulsion are involved), so we recomend to use this function up to 6 or 7 markers. For inbred-based populations, up to 10 or 11 markers can be ordered with this function, since linkage phase are known. The multipoint likelihood is calculated according to Wu et al. (2002b) (Eqs. 7a to 11), assuming that the recombination fraction is the same in both parents. Hidden Markov chain codes adapted from Broman et al. (2008) were used.

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

`best.ord`	a `matrix` containing the best orders.
`best.ord.rf`	a `matrix` with recombination frequencies for the corresponding best orders.
`best.ord.phase`	a `matrix` with linkage phases for the best orders.
`best.ord.like`	a `vector` with log-likelihood values for the best orders.
`best.ord.LOD`	a `vector` with LOD Score values for the best orders.
`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 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

marker.type for details about segregation types and make.seq.

## Not run: 
  #outcrossing example
  data(example.out)
  twopt <- rf.2pts(example.out)
  markers <- make.seq(twopt,c(12,14,15,26,28))
  (markers.comp <- compare(markers))
  (markers.comp <- compare(markers,verbose=TRUE))


## End(Not run)