| Class | Analysis and data manipulation command |
| Name | lod |
| 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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