onemap (version 2.0-1)

make.seq: Create a sequence of markers

Description

Makes a sequence of markers based on an object of another type.

Usage

make.seq(input.obj, arg=NULL, phase=NULL, twopt=NULL)

Arguments

input.obj

an object of class rf.2pts, group, compare, try or order.

arg

its value depends on the type of object input.obj. For an object rf.2pts, arg can be the string "all", resulting in a sequence with all markers in the raw data (generally done for grouping markers); other

phase

its value is also dependent on the type of input.obj. For an rf.2pts object, phase can be a vector with user- defined linkage phases (its length is equal to the number of markers minus one);

twopt

a string indicating the name of the object which contains the two-point information. This does not have to be defined by the user: it is here for compatibility issues when calling make.seq from inside other functions.

Value

• An object of class sequence, which is a list containing the following components:
• seq.num
  a vector containing the (ordered) indices of markers in the sequence, according to the input file.
• seq.phases
  a vector with the linkage phases between markers in the sequence, in corresponding positions. -1 means that there are no defined linkage phases.
• seq.rf
  a vector with the recombination frequencies between markers in the sequence. -1 means that there are no estimated recombination frequencies.
• seq.like
  log-likelihood of the corresponding linkage map.
• 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.

References

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.

See Also

compare, try.seq, order.seq and map.

Examples

data(example.out)
  twopt <- rf.2pts(example.out)

  all.mark <- make.seq(twopt,"all")
  all.mark <- make.seq(twopt,1:30) # same as above, for this data set
  groups <- group(all.mark)
  LG1 <- make.seq(groups,1)
  LG1.ord <- order.seq(LG1)
  (LG1.final <- make.seq(LG1.ord)) # safe order
  (LG1.final.all <- make.seq(LG1.ord,"force")) # forced order

  markers <- make.seq(twopt,c(2,3,12,14))
  markers.comp <- compare(markers)
  (base.map <- make.seq(markers.comp))
  base.map <- make.seq(markers.comp,1,1) # same as above
  (extend.map <- try.seq(base.map,30))
  (base.map <- make.seq(extend.map,5)) # fifth position is the best