nicemapd

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

Synopsis:

The nicemapd command is invoked as either one of :

• nicemapd Options
• nicemapd

Description:

The nicemapd 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 nearest 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 especially not be used when two data-sets have been merged with separate parameters 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 /homes/thomas/carthagene/test/Data/bc.cg}
CG> nicemapd

Map -1 : log10-likelihood =  -331.49
-------:
 Set : Marker List ...
   1 : MS13 MS14 MS11 MS10 MS9 MS8 MS7 MS6 MS5 MS4 MS3 MS2 MS1 MS12 MS15 MS16\
 MS18 MS17 MS19 MS20

See also:

• nicemapl (2.5.4)
• mfmapd (2.5.7)
• mfmapl (2.5.6)
• sem (2.5.2)