Class | Analysis and data manipulation command |
Name | set analysis |
Arguments | [imputed|observed] |
Includes imputed genotypes in generalized linear models fitted using the regress command. Genotypes are automatically reimputed each time regress is called. The idea of this is to allow multiple imputation association analysis. Imputation is performed using Sib-pair's single locus genotype MCMC sampler.
The regress command with imputed genotypes respects the set frequencies command, so that the population allele frequencies can be specified in advance. This allows appropriate estimation in samples ascertained on genotypes at the locus to be tested.
Example:
>> include williamsex.in >> reg CHD = ldl >> set analysis imputed >> set freq ldl 0.999 0.001 >> reg CHD = ldl >> reg CHD = ldl >> reg CHD = ldl
See also:
set frequencies | Specify allele frequencies |
gpe | Genotype probability estimates. |
regress | Generalized linear models. |
<< (set weight) | Up to index | >> (set burn-in) |