cgrobustness

Sets the reliability testing threshold for framework maps.

Synopsis:

The cgrobustness command is invoked as either:

• cgrobustness Options
• cgrobustness Threshold

Description:

The cgrobustness command sets the threshold used to verify if the current best known map is robust or not. A map $M$ is not robust if there exists another map $M'$ such that $L(M') > L(M) + \delta$, where $L(M)$ is the multipoint log-likelihood of $M$. A common value for the threshold $\delta$ is $-3.0$. When robustness checking is activated, each time a new map is inserted into the heap, the system verifies if the current best map is still robust. If not then it will stop any running search procedure because it has found a proof that the best known map is not robust enough. This is typically used when checking the reliability of a framework map using a cpu-intensive command such as flips or greedy in order to stop the search process as soon as the unreliability is proven.

Arguments:

• Options : -u to obtain the synopsys of the normal use, -h to print a one line description, -H to print a short help.
• Threshold: minimum log likelihood distance to the current best map.

Example:

CG> dsload Data/bc.cg
{1 f2 backcross 20 208 /homes/thomas/carthagene/test/Data/bc.cg}
CG> buildfw 3 3 {} 1

BuildFW, Adding  Threshold = 3.00, Saving Threshold = 3.00.

>>> Delta = 10.84 :

Map  0 : log10-likelihood =  -114.56
-------:
 Set : Marker List ...
   1 : MS4 MS9 MS12

>>> Delta = 9.73 , Id = 1,  Locus = MS1 :

Map  0 : log10-likelihood =  -155.67
-------:
 Set : Marker List ...
   1 : MS1 MS4 MS9 MS12

>>> Delta = 10.78 , Id = 7,  Locus = MS7 :

Map  0 : log10-likelihood =  -166.66
-------:
 Set : Marker List ...
   1 : MS1 MS4 MS7 MS9 MS12

>>> Delta = 13.30 , Id = 2,  Locus = MS2 :

Map  0 : log10-likelihood =  -178.48
-------:
 Set : Marker List ...
   1 : MS1 MS2 MS4 MS7 MS9 MS12

>>> Delta = 7.08 , Id = 16,  Locus = MS16 :

Map  0 : log10-likelihood =  -203.02
-------:
 Set : Marker List ...
   1 : MS1 MS2 MS4 MS7 MS9 MS12 MS16

>>> Delta = 11.51 , Id = 11,  Locus = MS11 :

Map  0 : log10-likelihood =  -207.54
-------:
 Set : Marker List ...
   1 : MS1 MS2 MS4 MS7 MS9 MS11 MS12 MS16

>>> Delta = 10.59 , Id = 18,  Locus = MS18 :

Map  0 : log10-likelihood =  -232.48
-------:
 Set : Marker List ...
   1 : MS1 MS2 MS4 MS7 MS9 MS11 MS12 MS16 MS18

>>> Delta = 8.70 , Id = 15,  Locus = MS15 :

Map  0 : log10-likelihood =  -237.17
-------:
 Set : Marker List ...
   1 : MS1 MS2 MS4 MS7 MS9 MS11 MS12 MS15 MS16 MS18

>>> Delta = 7.08 , Id = 5,  Locus = MS5 :

Map  0 : log10-likelihood =  -239.87
-------:
 Set : Marker List ...
   1 : MS1 MS2 MS4 MS5 MS7 MS9 MS11 MS12 MS15 MS16 MS18

>>> Delta = 4.08 , Id = 8,  Locus = MS8 :

Map  0 : log10-likelihood =  -248.48
-------:
 Set : Marker List ...
   1 : MS1 MS2 MS4 MS5 MS7 MS8 MS9 MS11 MS12 MS15 MS16 MS18

BuildFW, remaining loci test :
       |                          |
       |               1 1 1 1 1  |     Lod2pt         Dist2pt
       | 1 2 4 5 7 8 9 1 2 5 6 8  |  Left<-M->Right Left<-M->Right | 0->N  ...
     --|--------------------------|--------------------------------|-------...
   MS3 |  2 +                     |  47.62   35.05     0.6   5.7   |   21.0...
   MS6 |        + 3               |  15.41   17.32     4.5   1.6   |   30.5...
  MS10 |          2 0 + 0 3 3 2   |   7.22    3.61     0.0   0.0   |   44.9...
  MS13 |                + 0       |  11.91   18.66     8.4   0.0   |   53.7...
  MS14 |            2 1 0 0 0 + 1 |   3.61    0.00     0.0 345.4   |   71.6...
  MS17 |                      0 + |  15.95     -       0.0    -    |   94.4...
  MS19 |                      2 + |  27.14     -       2.8    -    |   94.4...
  MS20 |                      3 + |  22.88     -       5.0    -    |   94.4...

CG> cgrobustness -5

CG> greedy 1 0 1 20 0

Map -1 : log10-likelihood =  -248.48
-------:
 Set : Marker List ...
   1 : MS1 MS2 MS4 MS5 MS7 MS8 MS9 MS11 MS12 MS15 MS16 MS18
Run number 0
Current best map is not robust!
Aborted!

CG> heapsize 3

CG> heaprint

Map  0 : log10-likelihood =  -255.57
-------:
 Set : Marker List ...
   1 : MS1 MS2 MS5 MS4 MS7 MS8 MS9 MS11 MS12 MS15 MS16 MS18

Map  1 : log10-likelihood =  -252.56
-------:
 Set : Marker List ...
   1 : MS1 MS2 MS4 MS5 MS7 MS9 MS8 MS11 MS12 MS15 MS16 MS18

Map  2 : log10-likelihood =  -248.48
-------:
 Set : Marker List ...
   1 : MS1 MS2 MS4 MS5 MS7 MS8 MS9 MS11 MS12 MS15 MS16 MS18

CG>

See also:

• cgnotrobust (2.5.20)