polish

Checks map reliability by swapping pairs of markers.

Synopsis:

The polish command is invoked either as:

• polish Options
• polish

Description:

For all the markers in the current best known map in the heap, the polish command displaces each marker in all possible intervals and reports the difference in log-likelihood in a matrix. Each line and column corresponds to a marker and displays the difference in loglikelihood of the maps obtained by displacing the marker of the line to the direct right of the marker in the column. A negative number indicates a better map has been found.

All the maps considered are candidates to be inserted in the heap adn therefore any improvement obtained here is automatically memorized.

Arguments :

• Options : -u to obtain the synopsys of the normal use, -h to print a one line description, -H to print a short help.

Returns:

nothing.

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]

CG> nicemapl

Map -1 : log10-likelihood =  -148.06
-------:
 Set : Marker List ...
   1 : MS2 MS3 MS4 MS7 MS8 MS9 MS6 MS5 MS10

CG> polish

Local map analysis:

         MS2   MS3   MS4   MS7   MS8   MS9   MS6   MS5  MS10
      ------------------------------------------------------
  MS2 |-----   1.2  22.3  43.7  58.2  38.4  35.9  29.9  27.9
  MS3 |  1.2 -----  21.7  45.4  62.3  39.8  37.4  30.8  30.4
  MS4 |  9.0  21.7 -----  23.1  38.1  19.5  14.2  10.5  12.5
  MS7 | 21.0  44.3  23.1 -----  15.4   0.2   2.9   5.9  11.0
  MS8 | 30.2  62.9  42.3  15.4 -----   0.1  16.2  11.0  12.2
  MS9 | 26.6  57.9  40.1  15.9   0.1 -----  13.9   8.9   8.9
  MS6 |  7.1  24.4  10.6  -4.3  -1.8  13.9 -----   2.7   1.5
  MS5 |  7.8  24.6   2.8  -4.3   4.2  16.5   2.7 -----   1.4
 MS10 |  4.3  19.9   4.5   3.1  -0.9  -1.7  -1.7   1.4 -----
      ------------------------------------------------------

See also:

• flips (2.6.4)
• annealing (2.6.7)
• greedy (2.6.8)