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:

CG> dsload Data/rh.cg
{1 haploid RH 53 118 /homes/thomas/carthagene/test/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)