map_avoid_unlinked function

Repeat HMM if map find unlinked marker

map_avoid_unlinked(
  input.seq,
  size = NULL,
  overlap = NULL,
  phase_cores = 1,
  tol = 1e-04,
  parallelization.type = "PSOCK",
  max.gap = FALSE,
  global_error = NULL,
  genotypes_errors = NULL,
  genotypes_probs = NULL
)

Arguments

• input.seq: object of class sequence
• 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)
• tol: tolerance for the C routine, i.e., the value used to evaluate convergence.
• parallelization.type: one of the supported cluster types. This should be either PSOCK (default) or FORK.
• max.gap: the marker will be removed if it have gaps higher than this defined threshold in both sides
• global_error: single value to be considered as error probability in HMM emission function
• genotypes_errors: matrix individuals x markers with error values for each marker
• genotypes_probs: table containing the probability distribution for each combination of marker × individual. Each line on this table represents the combination of one marker with one individual, and the respective probabilities. The table should contain four three columns (prob(AA), prob(AB) and prob(BB)) and individuals*markers rows.

Returns

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.

Examples

data(onemap_example_out)
  twopt <- rf_2pts(onemap_example_out)

  markers <- make_seq(twopt,c(30,12,3,14,2)) # correct phases
  map_avoid_unlinked(markers)

  markers <- make_seq(twopt,c(30,12,3,14,2),phase=c(4,1,4,3)) # incorrect phases
  map_avoid_unlinked(markers)