build

This command is obsolete. It is largely superseded by the buildfw command which may also build comprehensive maps. It heuristically builds a relatively good comprehensive map using an incremental insertion procedure.

Synopsis:

The CarthaGene build command is invoked as either one of :

• build Options
• build NbMap

Description :

starting from the most tightly connected (maximum 2 points LOD) pair of markers, the loci whose mean LOD with already inserted markers is maximum is inserted at its best position. Actually, all best NbMap insertion points are kept. The process is repeated for all markers.

Arguments :

• Options : -u to obtain the synopsys of the normal use, -h to print a one line description, -H to print a short help.
• NbMap: the number of candidate maps kept at each iteration.

Returns:

nothing but all maps explored are candidate for the heap.

Example :

# we first load a data set
CG> dsload Data/rh.cg
{1 haploid RH 53 118 /homes/thomas/carthagene/test/Data/rh.cg}
# we perform group detection (output omitted)
CG> group 0.3 3
...
# we select group 10
CG> mrkselset [groupget 10]

# we use the command build (20 parallel maps)
CG> build 20

Build(20) : |||||||||

Map 14 : log10-likelihood =  -141.81
-------:
 Set : Marker List ...
   1 : G7 G12 G13 G16 G6 G5 G17 G18 G14

# and check the quality of the final map
CG> flips 9 0 0

Single Flip(window size : 9, threshold : 0.00).


Map -1 : log10-likelihood =  -141.81
-------:
 Set : Marker List ...
   1 : G7 G12 G13 G16 G6 G5 G17 G18 G14


 2 2 2 3 2 1 3 3 2  log10
 1 6 7 0 0 9 1 2 8   -141.81
[8 7 6 5 - 3 2 1 0]      0.00


# it should be Ok.

See also:

• buildfw (2.5.18)
• nicemapl (2.5.4)
• nicemapd (2.5.5)
• mfmapl (2.5.6)
• mfmapd (2.5.7)