nicemapl

Computes an intuitively nice marker ordering using 2-points LOD.

Synopsis:

The nicemapl command is invoked as either one of :

• nicemapl Options
• nicemapl

Description:

The nicemapl command orders the current list of active markers using a simple Nearest Neighbor heuristics. Starting from each marker successively, it builds a map by always selecting the marker with the strongest LOD as the next marker. The best map according to multipoint maximum likelihood is inserted in the heap.

Warning: since 2-points estimations are typically unavailable for some pairs of markers when data-sets are merged, this command will return very poor maps on such merged data. This command should be used preferably to nicemapd when some data-sets have been merged with separate parameter estimation (using mergor).

Arguments:

• Options : -u to obtain the synopsys of the normal use, -h to print a one line description, -H to print a short help.

Returns:

nothing.

Example:

CG> dsload Data/bc.cg
{1 f2 backcross 20 208 /home/tschiex/Dev/carthagene/doc/user/exemple/Data/b...
CG> nicemapl

Map -1 : log10-likelihood =  -344.26
-------:
 Set : Marker List ...
   1 : MS14 MS13 MS11 MS10 MS5 MS6 MS1 MS2 MS3 MS4 MS7 MS8 MS9 MS12 MS15 MS16\
 MS17 MS18 MS19 MS20

See also:

• sem (2.5.2)
• nicemapd (2.5.5)
• mfmapl (2.5.6)
• mfmapd (2.5.7)
• build (2.5.16)
• buildfw (2.5.18)