Simulate quantitative trait(s)


-var number

The phenotypic variance for the first trait. If this number is >0, the first quantitative trait will be simulated. This option should be used with -vp and -mu.
For example,

-var 100

The phenotypic variance for the first trait will be 100.

-vp number,number,...

The proportions of variance explained by QTL, polygenic effects, and shared environmental effects on the first trait. The first k numbers correspond to the proportions for the k QTL, the next number corresponds to the proportion for the polygenic effects, and the last number corresponds to the proportion for the shared environmental effects. For example, if 3 QTL are specified with -site.

-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.

-mu number

The population mean for the first trait.
For example,

-mu 150

The mean for the first trait value will be 150.

-var2 number
-vp2 number,number,...
-mu2 number

Same as options for the first trait. These are the options for the second trait.

-pintersect number

The proportion of intersection of polygenic sites for traits 1 and 2. The number should be between 0 and 1. SeqSIMLA simulates 1000 polygenic sites for traits 1 and 2. For correlated traits, the sites for traits 1 and 2 can overlap.
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.

--d
--r

SeqSIMLA by default assumes an additive model for the QTL. If --d is specified, dominant model will be used. If --r is specified, recessive model will be used. The models affect how genotypic values for the QTL are calculated. Assume aj is the genotypic value for a QTL j and dj is the dominance deviation.

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.

-sp_cor number

The correlation coefficient between spouses for the shared environmental effects on the first trait. The default value is 0.
For example,

-sp_cor 0.5

-po_cor number

The correlation coefficient between parent and offspring for the shared environmental effects on the first trait. The default value is 0.
For example,

-po_cor 0.2

-sib_cor number

The correlation coefficient between siblings for the shared environmental effects on the first trait. The default value is 0.
For example,

-sib_cor 0.2

-sp_cor2 number
-po_cor2 number
-sib_cor2 number

Similar to the correlations for the first trait, these three options specify the correlation coefficients between spouses, between parent and offspring, between siblings for the shared environmental effects on the second trait.

-sp_corb number

The correlation coefficient between spouses for the shared environmental effects between traits. The default value is 0.
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.

-po_corb number

The correlation coefficient between parent and offspring for the shared environmental effects between traits. The default value is 0.
For example,

-po_corb 0.3

-sib_corb number

The correlation coefficient between siblings for the shared environmental effects between traits. The default value is 0.
For example,

-sib_corb 0.3

-self_corb number

The correlation coefficient within the same person for the shared environmental effects between traits. The default value is 0.
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.

-extreme number,number

The option can be used to simulate threshold trait for the first trait. That is, a person's trait value will be greater or lower than a threshold. The first number specifies the upper bond and the second number specifies the lower bond of the thresholds. This option should be used with -proband.
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.

-extreme2 number,number

The option can be used to simulate threshold trait for the second trait. This option should be used with -extreme and -erelation.

-erelation 0/1,0/1

The option specifies the relationship between the threshold values for the first and second traits. The first value specifies the relationship for the upper bonds for traits 1 and 2. The second value specifies the relationship for the lower bonds for traits 1 and 2. The value 0 means an OR relationship and the value 1 means an AND relationship.
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.