Apply the batch mapping algorithm using overlapping windows.
map.overlapping.batches(input.seq, size = 50, overlap = 15,
fun.order = NULL, phase.cores = 1, ripple.cores = 1, verbosity = NULL,
max.dist = Inf, ws = 4, increase.every = 4, max.tries = 10,
min.tries = 0, seeds = NULL, optimize = "likelihood", ...)an object of class sequence.
The center size around which an optimum is to be searched
The desired overlap between batches
A function that is applied to each batch to improve
marker order. See ripple.ord
The number of parallel processes to use when estimating the phase of a marker. (Should be no more than 4)
The number of parallel processes to use when calculating alternative order.
A character vector that includes any or all of "batch", "order", "position", "time" and "phase" to output progress status information.
The maximum distance (in cM) two markers can have in a batch
before automatic reordering is triggered (given that fun.order was
set).
The window size that the reordering function should use
Increase the window size by one every n-th round when re-ordering.
The maximum number of re-ordering tries. Failing to order after max.tries outputs a warning.
The minimum number of re-ordering tries.
A vector of phase information used as seeds for the first batch
Either "likelihood" or "count". Passed to ripple.ord
in order to optimize the map's likelihood or the RECORD COUNT criterion.
Unless you are absolutely sure why, you should use "likelihood".
Other arguments passed to fun.order
A list with the first element Map being an object of class
sequence, which is a list containing the
following components:
a vector containing the
(ordered) indices of markers in the sequence, according to the input file.
a vector with the linkage phases between markers
in the sequence, in corresponding positions. -1 means that there are
no defined linkage phases.
a vector with the
recombination frequencies between markers in the sequence. -1 means
that there are no estimated recombination frequencies.
log-likelihood of the corresponding linkage map.
name of the object of class outcross with the raw
data.
name of the object of class rf.2pts with the
2-point analyses.
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. Further the user has the option of
setting fun.order to a function that tries different orders and
iteratively reorders markers to improve the map. See
ripple.ord for such an implementation. The ordering
function is triggered at least min.tries times per batch, or as
long as a batch has two markers with a distance greater than
max.dist.