onemap (version 3.0.0)

record: Recombination Counting and Ordering

Description

Implements the marker ordering algorithm Recombination Counting and Ordering (Van Os et al., 2005).

Usage

record(
  input.seq,
  times = 10,
  LOD = 0,
  max.rf = 0.5,
  tol = 1e-04,
  rm_unlinked = TRUE,
  size = NULL,
  overlap = NULL,
  phase_cores = 1,
  hmm = TRUE,
  parallelization.type = "PSOCK",
  verbose = TRUE
)

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 onemap with the raw data.

twopt

name of the object of class rf_2pts with the 2-point analyses.

Arguments

input.seq

an object of class sequence.

times

integer. Number of replicates of the RECORD procedure.

LOD

minimum LOD-Score threshold used when constructing the pairwise recombination fraction matrix.

max.rf

maximum recombination fraction threshold used as the LOD value above.

tol

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

rm_unlinked

When some pair of markers do not follow the linkage criteria, if TRUE one of the markers is removed and record is performed again.

size

The center size around which an optimum is to be searched

overlap

The desired overlap between batches

phase_cores

The number of parallel processes to use when estimating the phase of a marker. (Should be no more than 4)

hmm

logical defining if the HMM must be applied to estimate multipoint genetic distances

parallelization.type

one of the supported cluster types. This should be either PSOCK (default) or FORK.

verbose

A logical, if TRUE it output progress status information.

Author

Marcelo Mollinari,

Details

Recombination Counting and Ordering (RECORD) is an algorithm for marker ordering in linkage groups. It is not an exhaustive search method and, therefore, is not computationally intensive. However, it does not guarantee that the best order is always found. The only requirement is a matrix with recombination fractions between markers.

After determining the order with RECORD, the final map is constructed using the multipoint approach (function map).

References

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.

Van Os, H., Stam, P., Visser, R.G.F. and Van Eck, H.J. (2005) RECORD: a novel method for ordering loci on a genetic linkage map. Theoretical and Applied Genetics 112: 30-40.

See Also

make_seq and map

Examples

# \donttest{
  ##outcross example
  data(onemap_example_out)
  twopt <- rf_2pts(onemap_example_out)
  all_mark <- make_seq(twopt,"all")
  groups <- group(all_mark)
  LG1 <- make_seq(groups,1)
  LG1.rec <- record(LG1, hmm = FALSE)

  ##F2 example
  data(onemap_example_f2)
  twopt <- rf_2pts(onemap_example_f2)
  all_mark <- make_seq(twopt,"all")
  groups <- group(all_mark)
  LG1 <- make_seq(groups,1)
  LG1.rec <- record(LG1, hmm = FALSE)
  LG1.rec
# }