Sib-pair Command: lod


ClassAnalysis and data manipulation command
Namelod
Arguments <marker locus 1> <marker locus 2> [<recombination_distance>]

Performs two-point lod score linkage analysis for codominant markers. The algorithm is fairly slow in the presence of many missing genotypes.

Example:

>> include cavanaughex.in
>> lod D16S769 D16S3145

------------------------------------
Two-point lod score linkage analysis
------------------------------------

"D16S769" (7 alleles) v. "D16S3145" (9 alleles).

 LogLikelihood   LOD       Theta
--------------  ---------  -------
    -719.064        0.000   0.5000
    -731.374       -5.346   0.0001
    -704.595        6.284   0.0100
    -700.433        8.091   0.0250
    -698.596        8.889   0.0500
    -698.567        8.902   0.0750
    -699.298        8.584   0.1000
    -701.847        7.477   0.1500
    -705.064        6.080   0.2000
    -711.776        3.165   0.3000
    -717.038        0.880   0.4000

>> lod D16S769 D16S3145 0.0615

------------------------------------
Two-point lod score linkage analysis
------------------------------------

"D16S769" (7 alleles) v. "D16S3145" (9 alleles).

 LogLikelihood   LOD       Theta
--------------  ---------  -------
    -719.064        0.000   0.5000
    -698.451        8.952   0.0615

>> sho map

User specified marker map:

Marker         Pos (cM)   Theta
-----------    --------   -----
D16S769           53.71   0.329   26066263 (chr 16)
D16S3145          55.01   0.013   26784604 (chr 16)
[...]

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