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 ($<10$) 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 :

   CarthaGene version 1.2-LKH, Copyright (c) 1997-2010 (INRA).

   CarthaGene comes with ABSOLUTELY NO WARRANTY.
   CarthaGene is free software. You are welcome to redistribute it,
   under certain conditions. See the License file for information.

Type 'help' for help.

CG> dsload Data/bc.cg
{1 f2 backcross 20 208 /home/tschiex/Dev/carthagene/doc/user/exemple/Data/b...
CG> group 0.1 7

Linkage Groups :
---------------:
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 =  -129.39
-------:
 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 =  -129.39
-------:
 Set : Marker List ...
   1 : MS2 MS3 MS4 MS5 MS6 MS7 MS8 MS9 MS10


                 1  log10
 2 3 4 5 6 7 8 9 0   -129.39
[- - - - - - - 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

See also:

• polish (2.6.5)
• annealing (2.6.7)
• greedy (2.6.8)