cgstat

Displays some benchmarking statistics on CarthaGene and the Heap.

Synopsis:

The cgstat command is invoked either as:

• cgstat Options
• cgstat LOD-Threshold

Description:

The command cgstat displays some basic statistics on the software and the contents of the heap. It reports the total CPU-time consumed, the number of calls to the EM (Expectation/Maximization) algorithm and the number of maps in the heap within LOD-Threshold of the best known map in the heap.

For internal use only: if the data-set loaded is identified as a randomly generated test data-set, further statistics are reported: difference in log-likelihood of the best know map with the log-likelihood of the order used to generate the data, at what cpu-time stamp this map was found and if it is identical to the order used to generate the data.

Arguments:

• Options : -u to obtain the synopsys of the normal use, -h to print a one line description, -H to print a short help.
• LOD-Threshold: maximum difference in loglikelihood with the best known map.

Returns:

a list of these different statistics (some may be unapplicable when the data set used is not a benchmarking random data-set).

• a boolean that indicates whether the best map found is the correct (model) map.
• the total cpu-time used
• the difference of loglikelihood between the best maporder and the ``true'' order.
• the cpu-time stamp of the best known map.
• the number of maps in the heap whose loglikelihood is within LOD-Threshold of the best map.
• the number of EM calls overall.

Example:

# we load a dataset
CG> dsload Data/bc.cg
{1 f2 backcross 20 208 /homes/thomas/carthagene/test/Data/bc.cg}
#compute groups
CG> group 0.1 7
...
#and select group 4
CG> mrkselset [groupget 4]
...
# compute a first map
CG> nicemapd
...
# check the quality of this order
CG> flips 2 0 0
...
#check some statistics and ask for the number of maps within 1 of the optimum
CG> cgstat 1

Map  8 : log10-likelihood =  -135.41, log-e-likelihood =  -311.80
-------:

Data Set Number  1 :

      Markers        Distance    Cumulative  Distance   Theta       2pt
Pos  Id name         Haldane     Haldane     Kosambi    (%%age)      LOD

  1   2  MS2           0.6 cM      0.6 cM      0.6 cM     0.6 %%    47.6
  2   3  MS3           5.8 cM      6.4 cM      5.5 cM     5.5 %%    35.1
  3   4  MS4           3.6 cM     10.1 cM      3.5 cM     3.5 %%    21.1
  4   5  MS5           3.7 cM     13.8 cM      3.6 cM     3.6 %%    15.4
  5   6  MS6           1.6 cM     15.4 cM      1.6 cM     1.6 %%    17.3
  6   7  MS7           6.7 cM     22.1 cM      6.3 cM     6.3 %%    35.1
  7   8  MS8           2.5 cM     24.6 cM      2.5 cM     2.5 %%     7.4
  8  10 MS10           0.0 cM     24.6 cM      0.0 cM     0.0 %%     7.2
  9   9  MS9        ----------              ----------
                      24.6 cM                 23.6 cM


        9 markers, log10-likelihood =  -135.41
                   log-e-likelihood =  -311.80
Total CPU Time (secondes): 0.01
Number of calls to EM: 28
# of maps within -136.410765: 1
Current best LogLike is -135.410765 and worst is -159.395426
Reliability Threshold = 1e+100
Tolerance Threshold1 = 0.1
Tolerance Threshold2 = 0.001
{1 0.010000 1 0.000000 0.010000 1 28}

See also:

• cgrestart (2.8.5)
• heaprint (2.4.4)