map_avoid_unlinked {onemap}

Repeat HMM if map find unlinked marker

Description

Repeat HMM if map find unlinked marker

Usage

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.

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.

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)