map.overlapping.batches: Mapping overlapping batches

In bschiffthaler/BatchMap: Software for the Creation of High Density Linkage Maps in Outcrossing Species

Description

Apply the batch mapping algorithm using overlapping windows.

Usage

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",
  ...
)

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
fun.order	A function that is applied to each batch to improve marker order. See ripple.ord
phase.cores	The number of parallel processes to use when estimating the phase of a marker. (Should be no more than 4)
ripple.cores	The number of parallel processes to use when calculating alternative order.
verbosity	A character vector that includes any or all of "batch", "order", "position", "time" and "phase" to output progress status information.
max.dist	The maximum distance (in cM) two markers can have in a batch before automatic reordering is triggered (given that fun.order was set).
ws	The window size that the reordering function should use
increase.every	Increase the window size by one every n-th round when re-ordering.
max.tries	The maximum number of re-ordering tries. Failing to order after max.tries outputs a warning.
min.tries	The minimum number of re-ordering tries.
seeds	A vector of phase information used as seeds for the first batch
optimize	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

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. 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.

Value

A list with the first element Map being 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.

Secondly batches, a list of Maps for each of the batches.

Author(s)

Bastian Schiffthaler, [e-mail]

See Also

pick.batch.sizes, map

bschiffthaler/BatchMap documentation built on Dec. 16, 2019, 2:22 a.m.