Description Usage Arguments Value
This function orders markers within linkage groups using a simulated annealing heuristic. The underlying implementation is a C++ reimplementation of the fortran code arsa.f
from the seriation
package. The reimplementation allows for multithreading, and is therefore much faster. It also fixes a couple of bugs in the original code.
Parameters cool
and tmin
are standard simulated annealing parameters, and decreasing cool
increases the amount of computation effort. Parameter nReps
gives the number of independent replications of the simulated annealing algorithm to be used. The result of the best replication is then chosen.
Parameter maxMove
gives the maximum number of positions by which to shift a marker, as part of a step within the simulated annealing algorithm. The computational effort of determining whether a proposed move of a particular marker should be accepted, depends on the number of positions by which it is moved. So if the ordering is already approximately correct at the start of the algorithm, proposals that move markers by large distances are expensive, and also unneccessary. These types of proposed changes to the ordering can be avoided by setting maxMove
to some positive value, maybe one tenth of the number of markers.
Parameter effortMultiplier
simply increases or decreases the amount of computational effort. A value of 0.5 requires half as much effort, a value of 1.0 uses the default amount of effort, and a value of 2.0 requires twice as much computational effort.
Parameter randomStart
controls the starting point of each replication of the algorithm. If this parameter is TRUE, then every replication starts form an independent random ordering. If this parameter is FALSE, then every replication starts from the marker ordering given in the input object.
1 2 3 4 5 6 7 8 9 10 | orderCross(
mpcrossLG,
cool = 0.5,
tmin = 0.1,
nReps = 1,
maxMove = 0,
effortMultiplier = 1,
randomStart = TRUE,
verbose = FALSE
)
|
mpcrossLG |
An object of class |
cool |
Rate of cooling |
tmin |
Minimum temperature |
nReps |
Number of independent replications of the simulated annealing algorithm |
maxMove |
Maximum number of positions by which to shift a single marker, as part of the simulated annealing. A value of zero indicates no limit. |
effortMultiplier |
Multiplier for the amount of computational effort |
randomStart |
If TRUE, start from the current ordering |
verbose |
If TRUE, generate more detailed output |
An object of class mpcrossLG
, identical to the input except with the markers rearranged.
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