rcd {onemap}

Rapid Chain Delineation

Description

Implements the marker ordering algorithm Rapid Chain Delineation (Doerge, 1996).

Usage

rcd(
  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 rcd 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

Rapid Chain Delineation (RCD) 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. Next is an excerpt from QTL Cartographer Version 1.17 Manual describing the RCD algorithm (Basten et al., 2005):

The linkage group is initiated with the pair of markers having the smallest recombination fraction. The remaining markers are placed in a “pool” awaiting placement on the map. The linkage group is extended by adding markers from the pool of unlinked markers. Each terminal marker of the linkage group is a candidate for extension of the chain: The unlinked marker that has the smallest recombination fraction with either is added to the chain subject to the provision that the recombination fraction is statistically significant at a prespecified level. This process is repeated as long as markers can be added to the chain.

After determining the order with RCD, 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

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.

Author(s)

Gabriel R A Margarido, [e-mail]

References

Basten, C. J., Weir, B. S. and Zeng, Z.-B. (2005) QTL Cartographer Version 1.17: A Reference Manual and Tutorial for QTL Mapping.

Doerge, R. W. (1996) Constructing genetic maps by rapid chain delineation. Journal of Quantitative Trait Loci 2: 121-132.

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.

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.rcd <- rcd(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.rcd <- rcd(LG1, hmm = FALSE)
  LG1.rcd