frameworkmst

Builds a framework map (only on Linux computers).

Synopsis :

The CarthaGene frameworkmst command is invoked as either one of :

• frameworkmst Options
• frameworkmst Delta ChangeSel

Description :

The frameworkmst command builds a framework map by selecting a subset of the current markers based on constrained maximum spanning tree algorithm. The robustness of the resulting map is controlled by the parameter Delta. It ensures that it does not exist any other map containing the same set of markers and with a different order such that its 2-pt log10-likelihood is greater than the framework map likelihood minus Delta. For instance if Delta is equal to 3, then any other map is 1000 less likely. If ChangeSel is equal to 1 then the best framework map is inserted into the Carthagene heap.

Arguments :

• Options : -u to obtain the synopsis of the normal use, -h to print a one line description, -H to print a short help.
• Delta: the minimum difference in log-likelihood between the framework map and any other map with the same marker selection.
• ChangeSel: if equal to 1 then the best framework map is inserted into the Carthagene heap (modifying the current marker list).

Returns :

nothing.

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/rh02_true.id
{1 haploid RH 427 88 /home/tschiex/Dev/carthagene/doc/user/exemple/Data/rh0...
CG>

# merge markers with similar RH vectors
CG> mrkmerges

CG>

# build a framework map such that any other map is 100 less likely
# and update the current marker selection to this framework map
CG> frameworknmst 2 1
All TSP costs multiplied by 1000.
0 (109): 12 8 7 33 34 30 31 27 23 21 19 14 4 47 53 60 61 63 68 69 72 65 73 ...

Map -1 : log10-likelihood =  -585.09
-------:
 Set : Marker List ...
   1 : 12 8 7 33 34 30 31 27 23 21 19 14 4 47 53 60 61 63 68 69 72 65 73 79...

CG>

See also:

• frameworknmst (uses normalized 2-pt log10-likelihood)
• framework (2.5.23)