Subsections

flips

Applies all possible permutations in a sliding window on the current best map and reports likelihood variations.

Synopsis:

The flips command is invoked either as:

• flips Options
• flips Size LOD-Threshold Iterative

Description:

The flips command applies all possible permutations in a sliding window of a given Size on the current best available map (the best map in the heap). If the map obtained has a loglikelihood within LOD-Threshold of the loglikelihood of the original map, then the permutation that lead to this map is displayed. If a new improved map is found, the filps command can be automatically iterated using a value of 1 for the last argument.

Note that this command can be also used to perform exhaustive search of all possible order when a small () number of markers is active by simply specifying the number of active markers as the sliding window size.

Arguments:

• Options : -u to obtain the synopsys of the normal use, -h to print a one line description, -H to print a short help.
• Size : the size of the sliding window (cannot exceed 9),
• LOD-Threshold: the maximum difference of loglikelihood with the best map to report the permutation,
• Iterative: a boolean that indicates whether the flips command should be iterated as long as a new improved map has been found.

Example :

```CG> dsload Data/bc.cg
{1 f2 backcross 20 208 /homes/thomas/carthagene/test/Data/bc.cg}
CG> group 0.1 7

---------------:
LOD threshold=7.00
Distance threshold=10.00:

Group ID : Marker ID List ...
1 : 17 19 20 18
2 : 14
3 : 11 13 12 16 15
4 : 2 4 3 7 6 5 9 10 8
5 : 1
5
CG> mrkselset [groupget 4]

# run this heuristic
CG> nicemapd

Map -1 : log10-likelihood =  -135.41
-------:
Set : Marker List ...
1 : MS2 MS3 MS4 MS5 MS6 MS7 MS8 MS9 MS10

# the reliability of the result with a large flip
CG> flips 9 1 1

Repeated Flip(window size : 9, threshold : 1.00).

Map -1 : log10-likelihood =  -135.41
-------:
Set : Marker List ...
1 : MS2 MS3 MS4 MS5 MS6 MS7 MS8 MS9 MS10

1  log10
2 3 4 5 6 7 8 9 0   -135.41
[- - - - - - - 8 7]     -0.00
[7 8 6 5 - 3 2 1 0]     -0.00
[8 7 6 5 - 3 2 1 0]      0.00

# the map was not optimal
```