parmap: A parallelized version of map function

Description

Based on the strategy propoused by Schiffthaler et al. the markers of a linkage group with pre-defined order are divided in user defined batches with overlap markers between them. Each batch runs in a different core which increase the speed of the genetic distances estimation. The distances and phases of the previous batch are considered to joint the batches. Also, it is possible to store the differences between the genetic distances between the overlaped markers as a measure of the process quality. In other words, if these differences are to too high, you can considered that divide the group in batch did not compromise the distance estimation.

Usage

parmap(
  input.seq = NULL,
  cores = 3,
  overlap = 4,
  tol = 1e-04,
  avoid_link_errors = TRUE,
  export_diff = FALSE,
  verbose = TRUE
)

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.

Arguments

input.seq: an object of class sequence.
cores: an integer defining the number of cores to be used and also the number of batches generated
overlap: number of markers overlapping between batches
tol: tolerance for the C routine, i.e., the value used to evaluate convergence.
avoid_link_errors: logical. If TRUE markers which do not reach the linkage criteria are removed of the sequence and the distances are automatically reestimated. If FALSE an error stops the algorithm it find these markers.
export_diff: If TRUE also returns (in the first level of the list) the differences in genetic distances between overlaped markers
verbose: A logical, if TRUE its output progress status information.

Author

Cristiane Taniguti chtaniguti@tamu.edu

References