Description Usage Arguments Details Value Author(s) See Also
View source: R/overlapping.batches.R
Apply the batch mapping algorithm using overlapping windows.
1 2 3 4 |
input.seq |
an object of class |
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 |
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 |
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 |
... |
Other arguments passed to |
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
.
A list with the first element Map
being an object of class
sequence
, which is a list containing the
following components:
seq.num |
a |
seq.phases |
a |
seq.rf |
a |
seq.like |
log-likelihood of the corresponding linkage map. |
data.name |
name of the object of class |
twopt |
name of the object of class |
Secondly batches
, a list of Map
s for each
of the batches.
Bastian Schiffthaler, bastian.schiffthaler@umu.se
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