try.seq {onemap}R Documentation

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

Description

For a given linkage map and an additional marker, this function estimates parameters for all possible maps including the new marker, while keeping the base linkage map inaltered.

Usage

try.seq(w,mrk,tol=10E-5,verbose=FALSE)

## S3 method for class 'try':
print(x,j=NULL, ...)

Arguments

w 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.
verbose if FALSE (default), simplified output is displayed. if TRUE, detailed output is displayed.
x an object of class try.
j if NULL (default), output is a summary of the results for all possible positions of the additional marker. Otherwise, an integer makes detailed output to be printed for the corresponding position. This integer must be less than or equal to the length of the original sequence plus 1.
... further arguments, passed to other methods. Currently ignored.

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

Author(s)

Marcelo Mollinari, mmollina@esalq.usp.br

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.

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 and compare.

Examples

## Not run: 
  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)

[Package onemap version 1.0-1 Index]