onemap (version 1.0-0)

order.seq: Search for the best order of markers combining compare and try.seq functions

Description

For a given sequence of markers, this function first uses the compare function to create a framework for a subset of informative markers. Then, it tries to map remaining ones using the try.seq function.

Usage

order.seq(w,n.init=5,THRES=3,touchdown=FALSE,tol=10E-5)

Arguments

w

an object of class sequence.

n.init

the number of markers to be used in the compare step (defaults to 5).

THRES

threshold to be used when positioning markers in the try.seq step.

touchdown

logical. If FALSE (default), the try.seq step is run only once, with the value of THRES. If TRUE, try.seq runs with THRES and then once more, with THRES-1.

tol

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

Value

• An object of class order, which is a list containing the following components:
• ord
  an object of class sequence containing the "safe" order.
• mrk.unpos
  a vector with (possibly) unpositioned markers.
• LOD.unpos
  a matrix with LOD-Scores for unmapped markers, if any, for each position in the "safe" order.
• THRES
  the same as the input value, just for printing.
• ord.all
  an object of class sequence containing the "forced" order, i.e., the best order with all markers.
• 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.

Details

After running the compare and try.seq steps, which result in a "safe" order, markers that could not be mapped are "forced" into the map, resulting in a map with all markers positioned.

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, compare and try.seq.

Examples

data(example_out)
  twopt <- rf.2pts(example_out)
  all.mark <- make.seq(twopt,"all")
  groups <- group(all.mark)
  LG2 <- make.seq(groups,2)
  LG2.ord <- order.seq(LG2,touchdown=TRUE)
  LG2.ord
  make.seq(LG2.ord) # get safe sequence
  make.seq(LG2.ord,"force") # get forced sequence