Sib-pair Command: simulate qtl


ClassAnalysis and data manipulation command
Namesimulate 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


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