|Class||Data Declaration command|
|Arguments||<quantitative trait> [merlin]|
|error <threshold> <minimum markers>|
Declares which variable identifies twins. All individuals within a pedigree with the same nonmissing value of this variable are taken to be part of the same twin sibship (twin pair or higher order multiple). Different values indicate different twin pairs within the same family.
If the merlin coding has been specified, odd numbers indicate MZ twins, and even numbers DZ twins. For the default coding, nonzero values indicate MZ twins, and DZ twins can be indicated using a zero value for the indicator. If a zygosity indicator was declared in a MERLIN data file (see read locus), this automatically toggles use of the MERLIN encoding.
The zygosity indicator variable must be declared as a quantitative trait using the set locus command; this can be before or after the set twin statement. The zygosity indicator variable can be changed at any time.
This information is used to write out MZ twin indicators to the pedigree files used by MENDEL, MERLIN and SOLAR, to test for marker inconsistencies, and carry out classical twin analyses.
The error modifier shows and allows setting of the quick genotype discordance test (see test duplicates). The first argument is the allowed mistyping (ie discordance) rate for genotypes compared between putative genetically identical pairs of samples. This defaults to 0.005, which is acceptable for SNP or sequence markers. The second argument determines how many markers must be present before the comparison is made, defaulting to 100 markers.
>> set locus mzdz qua >> set twin mzdz NOTE: The phenotype "mzdz" indicates monozygotic (twin) sibships. >> set twin error Monozygotic twin or duplicate mistyping rate = .5000E-02 Minimum number of markers to be used = 100 NOTE: The phenotype "mzdz" indicates monozygotic (twin) sibships.
|test duplicates||Search/test for MZ twins or duplicate samples using marker concordance.|
|mztwin||MZ pair genotype discordance | drop one member|
|twin||Classical twin analysis|
|kendalltau||Twin survival analysis|
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