map_overlapping_batches {onemap}

Mapping overlapping batches

Description

Apply the batch mapping algorithm using overlapping windows.

Usage

map_overlapping_batches(
  input.seq,
  size = 50,
  overlap = 15,
  phase_cores = 1,
  verbose = FALSE,
  seeds = NULL,
  tol = 1e-04,
  rm_unlinked = TRUE,
  max.gap = FALSE,
  parallelization.type = "PSOCK"
)

Arguments

input.seq

an 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)

verbose

A logical, if TRUE its output progress status information.

seeds

A vector of phase information used as seeds for the first batch

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 map is performed again.

max.gap

the marker will be removed if it have gaps higher than this defined threshold in both sides

parallelization.type

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

Details

This algorithm implements the overlapping batch maps for high density marker sets. The mapping problem is reduced to a number of subsets (batches) which carry information forward in order to more accurately estimate recombination fractions and phasing. It is a adapted version of map.overlapping.batches function of BatchMap package. The main differences are that this onemap version do not have the option to reorder the markers according to ripple algorithm and, if the it finds markers that do not reach the linkage criterias, the algorithm remove the problematic marker and repeat the analysis. Than, the output map can have few markers compared with the input.seq.

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 outcross with the raw data.

twopt

name of the object of class rf.2pts with the 2-point analyses.

See Also

pick_batch_sizes, map