| Class | Analysis and data manipulation command |
| Name | simulate qtl |
| Arguments | <trait> <marker> [<h2>] |
The data for the named autosomal marker is replaced by simulated genotype data that is generated conditional on the trait values and the genetic model for the trait. The model for the QTL is taken from the results of the set sml command, and the residual heritability is specified as the last argument to the command.
Binary traits are modelled under the multifactorial threshold model, and quantitative traits are not currently supported.
The simulation is carried out by simple rejection sampling, and so performance will deteriorate with increasing sample size, and with difficulty of the model.
Example:
>> include linclex.in >> set loc trait marker Creating new variable "trait". >> set sml 0.1 0.9999 0.0001 0.0001 SML model: P(A)=0.100000 Pen(AA)=1.000 Pen(AB)=0.000 Pen(BB)=0.000 >> sim qtl lincl trait 0.0 Trait prevalence = 0.0101 QTL allele frequency = 0.1000 QTL penetrances = 0.9999 0.0001 0.0001 Trait MFT heritability = 0.0000 Affection 1/1 1/2 2/2 Total Freq ---------- ------ ------ ------ -------- ------ Unknown 0 0 0 0 0.0000 Unaffected 0 40 16 56 0.3571 Affected 16 0 0 16 1.0000 Total rejection samples= 15105 Elapsed time = 0.05 s