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7.6.4 Autozyg computational parameters

set markers K data N1 M11 M12 ... [N2 M21 M22 ...] ...

Individuals with at least one observed marker are named, together with their marker genotypes. The number of allele pairs for an individual is the same as the number of markers mapped on the chromosome. Marker loci not observed for an individual are given alleles `0 0'. (Those individuals with no observed markers need not be included in this statement.) In the example, there are 5 markers mapped for the chromosome:
 
set markers 5 data   343   1 3  1 3  1 3  1 3  1 3
                     331   3 4  3 4  3 4  3 4  3 4
                     334   2 3  2 3  2 3  2 3  2 3
                     431   3 4  3 4  3 4  3 4  3 4
                     531   3 4  3 3  0 0  3 3  3 3

set trait data (genotypic | phenotypic)

Trait data is specified as genotypic or phenotypic (discrete); the default is genotypic.

set [component M] affected individuals N1 N2 ...

lm_pval needs to know which members of the pedigree are affected with the disease: there are two ways to specify this. Affected individuals (for at least one component) may be named in this statement. Or, use the following statement if the affected individuals are to be determined from the pedigree data file.

set affected individuals trait K

Here, lm_pval is to determine the affected individuals from the trait data in the pedigree file. A trait genotypic code of 3 (genotype (1 2) or (2 1)) or 4 (genotype (2 2)) indicates an affected individual. The trait number, K, determines the position of this genotypic code in the pedigree records (see Pedigree file description statements.


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