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:

   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> buildfw 3 3 {} 1

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

>>> Delta = 46.28 :

Map  0 : log10-likelihood =   -14.70
-------:
 Set : Marker List ...
   1 : MS8 MS10 MS14

BuildFW, remaining loci test :
       |        |
       |   1 1  |     Lod2pt         Dist2pt
       | 8 0 4  |  Left<-M->Right Left<-M->Right | 0->N    N->M | Weight Nb...
     --|--------|--------------------------------|--------------|----------...
   MS1 |2   2 + |  -0.00     -     345.4    -    |   15.5 345.4 |     4    ...
   MS2 |+   3 2 |    -     15.26      -   23.8   |   -     23.8 |     5    ...
   MS3 |+     3 |    -     15.07      -   25.5   |   -     25.5 |     3    ...
   MS4 |+ 1 2 3 |    -     22.84      -   14.5   |   -     14.5 |     6    ...
   MS5 |  + 1 2 |  12.33    4.02    14.2   5.6   |    0.0   2.3 |     3    ...
   MS6 |  3 1 + |   1.05     -      22.6    -    |   15.5  22.6 |     4    ...
   MS7 |2 + 1 3 |  35.05    5.05     5.7  10.8   |    0.0   1.1 |     6    ...
   MS9 |  + 0 1 |  40.82    7.22     1.9   0.0   |    0.0   3.3 |     1    ...
  MS11 |  1 0 + |   3.61     -       0.0    -    |   15.5   0.0 |     1    ...
  MS12 |  2 0 + |   3.61     -       0.0    -    |   15.5   0.0 |     2    ...
  MS13 |    0 + |   6.02     -       0.0    -    |   15.5   0.0 |     0    ...
  MS15 |  3 0 + |   0.00     -     345.4    -    |   15.5 345.4 |     3    ...
  MS16 |  2 0 + |   3.61     -       0.0    -    |   15.5   0.0 |     2    ...
  MS17 |    + 0 |   1.09    1.51    31.8   0.0   |    3.3  12.2 |     0    ...
  MS18 |    2 + |   0.00     -     345.4    -    |   15.5 345.4 |     2    ...
  MS19 |1   3 + |   0.45     -      34.7    -    |   15.5  34.7 |     4    ...
  MS20 |    3 + |   0.71     -      45.8    -    |   15.5  45.8 |     3    ...

CG> cgrobustness -5

CG> greedy 1 0 1 20 0

Map -1 : log10-likelihood =   -14.70
-------:
 Set : Marker List ...
   1 : MS8 MS10 MS14
Run number 0
Current best map is not robust!
Aborted!

CG> heapsize 3

CG> heaprint

Map  0 : log10-likelihood =   -60.98
-------:
 Set : Marker List ...
   1 : MS10 MS8 MS14

Map  1 : log10-likelihood =   -17.48
-------:
 Set : Marker List ...
   1 : MS8 MS14 MS10

Map  2 : log10-likelihood =   -14.70
-------:
 Set : Marker List ...
   1 : MS8 MS10 MS14

CG>

See also:

• cgnotrobust (2.5.21)