group

Computes linkage groups in a data-set.

Synopsis:

The group command is invoked as either:

• group Options
• group Dist-Threshold LOD-Threshold

Description:

The group command computes cluster of markers, trying to identify linkage groups. The clustering is performed by putting in the same cluster any two markers such that their estimated two-points distance (using Haldane for genetic data) and their two-points LOD is respectively smaller than Dist-Threshold and larger than LOD-Threshold. This analysis is transitive in the sense that if there is reason to cluster together markers $A$ and $B$ on one side and markers $B$ and $C$ on another, then all threee markers will be put together (whether there is evidence for or against putting $A$ and $C$ together). Parameters should be typically adjusted to get a number of linkage groups consistent with the number of chromosomes in the organism.

Arguments:

• Options : -u to obtain the synopsys of the normal use, -h to print a one line description, -H to print a short help.
• Dist-Threshold: the maximum two-point distance (Haldane/Ray).
• LOD-Threshold: the minimum two-point LOD.

Returns:

the number of linkage groups detected.

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/rh.cg
{1 haploid RH 53 118 /home/tschiex/Dev/carthagene/doc/user/exemple/Data/rh.cg}
CG> group 0.5 3

Linkage Groups :
---------------:
LOD threshold=3.00
Distance threshold=50.00:

 Group ID : Marker ID List ...
        1 : 13 35 14
        2 : 10 18 17 16 15 11 12
        3 : 7
        4 : 6 53 52 8 51 50 9
        5 : 4 34 33 24 23 5 25
        6 : 3 32 29 31 30 28 27 26 20 19 21 22
        7 : 2 49 48 47 46 45 44 43 42 38 37 40 39 36 41
        8 : 1
8
CG>

See also:

• groupget (2.3.19)