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:

CG> dsload Data/bc.cg
{1 f2 backcross 20 208 /homes/thomas/carthagene/test/Data/bc.cg}
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 =  -154.08
-------:
 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)