try.seq: 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, \dots)

Arguments

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.

an object of class try.

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

...

further arguments, passed to other methods. Currently ignored.

Value

An object of class try, which is a list containing the following components:
orda list containing results for every linkage map estimated. These results include linkage phases, recombination frequencies and log-likelihoods.
LODa 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.orda matrix with the orders of all linkage maps.
data.namename of the object of class outcross with the raw data.
twoptname 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.

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

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