dsbplambda

Replaces the traditional criterion by the comparative mapping criterion for a given order data set.

Synopsis:

The dsbplambda command is invoked as:

• dsbplambda SetID CoefAutoFit NewLambdaValue

Description:

The dsbplambda command sets the lambda parameter value used in the definition of the comparative mapping criterion. The parameter SetId corresponds to the reference order dataset numerical id. Set the CoefAutoFit parameter to 1 in order to replace the traditional criterion by the comparative mapping criterion. Then, all the Carthagene map printing, building or improving commands will use this new criterion. By default, set the NewLambdaValue parameter to 1.

Arguments:

• SetId: the numerical id of the reference order dataset.

• CoefAutoFit : must be set to 1.

• NewLambdaValue : it corresponds to the expected number of breakpoints between the true order and the reference order given by dataset SetId. In general, this number of breakpoints is unknown, and it should be set to 1, or preferably to the minimum number of obligate breakpoints (the number of segments minus one in the reference order dataset) if greater than one.

Returns:

the previous lambda parameter value (default value is one).

Example:

CG> dsload Data/rh1_true.cg
{1 haploid RH 110 93 /home/tschiex/Dev/carthagene/doc/user/exemple/Data/rh1...
CG> dsload Data/order1_ref.cg
{2 order 110 /home/tschiex/Dev/carthagene/doc/user/exemple/Data/order1_ref.cg}
CG> dsmergor 1 2
{3 merged by order 110 93}
#select the comparative mapping criterion
CG> dsbplambda 2 1 1
New coefficient factor value is -3.356208.
1.0
#find a first good map
CG> lkh 1 -1
[-1015.90]
Best map with log10-likelihood = -1015.90
TSP: optimum= 954.887000 lowerbound= 954.107400 gap= 0.081710% totaltime= 0.36

Map -1 : log10-likelihood = -1015.90
-------:
 Set : Marker List ...
   1 : UniSTS158779 UniSTS164109 UniSTS158781 UniSTS158776 UniSTS207126 Uni...
   2 : UniSTS158779 UniSTS164109 UniSTS158781 UniSTS158776 UniSTS207126 Uni...

#try to improve this map (could be very slow depending on the last paramete...
CG> greedy 1 0 5 10 5

Map -1 : log10-likelihood = -1015.90
-------:
 Set : Marker List ...
   1 : UniSTS158779 UniSTS164109 UniSTS158781 UniSTS158776 UniSTS207126 Uni...
   2 : UniSTS158779 UniSTS164109 UniSTS158781 UniSTS158776 UniSTS207126 Uni...
Run number 0
------
[-1015.34]
[-1015.00]
[-1014.44]
[-1013.91]-----------------------------------------------------------------...

#show the best map in the heap
CG> bestprint

Map 13 : log10-likelihood = -1013.91
-------:
 Set : Marker List ...
   1 : UniSTS158781 UniSTS164109 UniSTS158779 UniSTS158776 UniSTS207126 Uni...
   2 : UniSTS158781 UniSTS164109 UniSTS158779 UniSTS158776 UniSTS207126 Uni...
13
CG>

See also:

The description of how to build a reference order dataset in the 'Formatting the data' section.