ug: Unidirectional Growth

In onemap: Construction of Genetic Maps in Experimental Crosses

Unidirectional Growth

Description

Implements the marker ordering algorithm Unidirectional Growth (Tan & Fu, 2006).

Usage

ug(
  input.seq,
  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
)

Arguments

input.seq	an object of class sequence.
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 ug 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.

Details

Unidirectional Growth (UG) 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 UG, the final map is constructed using the multipoint approach (function map).

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	object of class onemap with the raw data.
twopt	object of class rf_2pts with the 2-point analyses.

Author(s)

Marcelo Mollinari, [e-mail]

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.

Tan, Y. and Fu, Y. (2006) A novel method for estimating linkage maps. Genetics 173: 2383-2390.

See Also

make_seq, map

Examples

  #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.ug <- ug(LG1)

  #F2 example
  data(mapmaker_example_f2)
  twopt <- rf_2pts(mapmaker_example_f2)
  all_mark <- make_seq(twopt,"all")
  groups <- group(all_mark)
  LG1 <- make_seq(groups,1)
  LG1.ug <- ug(LG1)
  LG1.ug

onemap documentation built on Nov. 26, 2022, 9:05 a.m.