Description Usage Arguments Details Value See Also

Orders markers within linkage groups using two-point or multipoint probabilities. Two-point ordering is based on estimated recombination fractions; multi-point ordering is based on R/qtl ripple function.

1 2 3 4 5 |

`object` |
Object of class |

`chr` |
Selected chromosomes or linkage groups to order |

`type` |
Which type of ordering to perform - two-point or multipoint |

`rm.rf` |
Flag for whether to remove recombination fraction values from 2-pt ordering which have missing values |

`window` |
Window size for multipoint ordering |

`repeats` |
Number of times to repeat multipoint ordering |

`mapfx` |
Map function to use to compute final cM positions |

`criterion` |
Criterion used in 2-pt ordering to determine best order |

`missfx` |
Function to use to fill missing
recombination fractions. See |

`...` |
Additional arguments |

*Two-point ordering*

To use the two-point
ordering, the recombination fractions between all pairs
of markers must first be estimated. If there are missing
values in this matrix, the markers with the largest
number of missing values will be removed until there are
no missing values left. These markers will not be used in
the ordering and are recommended to be inserted into the
resulting framework map using `add3pt`

later.

Multiple methods are used to investigate optimal
two-point orderings. These are taken from the package
`seriation`

and include simulated annealing,
hierarchical clustering, and traveling salesman solver.
The orders are compared on the basis of the argument
`criterion`

. Thus the total path length, or sum of
adjacent recombination fractions can be minimized; or the
number of Anti-Robinson events/deviations; or the number
of crossovers; or the sum of the adjacent two-point LOD
scores.

*Multi-point ordering*

The multi-point ordering
assumes that there is a pre-existing map, and then
repeatedly applies the ripple function in R/qtl to
investigate local permutations of the order. These
orderings are constrained by the arguments `window`

and `repeats`

, which determine how large the
perturbations are and how many are considered. Large
values of `window`

are very time consuming;
recommended values are 5 or less, due to the number of
permutations which must be considered. Large values of
`repeats`

will eventually converge to an ordering in
which all local rearrangements of size `window`

have
been optimized with respect to the number of crossovers.

The original object with a new map component. Any pre-existing map will be retained as component $oldmap.

`mpestrf`

,
`mpgroup`

,
`add3pt`

,
`seriate`

,
`ripple`

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