For example,

-var 100

The phenotypic variance for the first trait will be 100.

-vp 0.05,0.1,0.15,0.2,0.3

The proportions of variance explained by the 3 QTL are 0.05, 0.1, and 0.15. The proportion for the polygenic effects is 0.2, and the proportion for the shared environmental effects is 0.3. The proportion for the individual-specific environmental effects is 1-0.05-0.1-0.15-0.2-0.3=0.2. Therefore, if the total phenotypic variance is 100 specified with -var, the variance explained by the 3 QTL will be 5, 10, and 15. The variance explained by the polygenic effects, the shared environmental effects, and the individual-specific environmental effects are 20, 30, and 20, respectively.

For example,

-mu 150

The mean for the first trait value will be 150.

-vp2 number,number,...

-mu2 number

For example,

-pintersect 0.8

80% of polygenic sites for the second trait will be the same as the polygenic sites for the first trait. The rest (20%) of the sites for the second trait will be independently simulated.

--r

Additive model:

Dominant model:

Recessive model:

where pj and qj are the allele frequencies for the two alleles at j and Vj is the variance explained by j.

For example,

-sp_cor 0.5

For example,

-po_cor 0.2

For example,

-sib_cor 0.2

-po_cor2 number

-sib_cor2 number

For example,

-sp_corb 0.3

Assume persons A and B are spouses. Then the correlation for the shared environmental effects between A's first trait and B's second trait will be 0.3. Also the correlation for the shared environmental effects between A's second trait and B's first trait will be 0.3.

For example,

-po_corb 0.3

For example,

-sib_corb 0.3

For example,

-self_corb 0.3

The correlation for the shared environmental effects between the first and second traits for a person will be 0.3.

For example,

-extreme 140,80

The individuals with affection status 2 in the proband file will have trait values > 140 for the first trait. The individuals with affection status 1 in the proband file will have trait values < 80 for the first trait.

For example,

-extreme 140,80 -extreme2 60,30 -erelation 0,1

The individuals with affection status 2 in the proband file will have trait values > 140 for the first trait OR > 60 for the second trait. The individuals with affection status 1 in the proband file will have trait values < 80 for the first trait AND < 30 for the second trait.

Another example,

-extreme 140,80 -extreme2 60,30 -erelation 1,1

The individuals with affection status 2 in the proband file will have trait values > 140 for the first trait AND > 60 for the second trait. The individuals with affection status 1 in the proband file will have trait values < 80 for the first trait AND < 30 for the second trait.