Sib-pair Command: set frequencies

ClassAnalysis and data manipulation command
Nameset frequencies
Arguments <marker> [(<allele 1 frequency>...<allele N frequency>) |
(<allele 1 name> <allele 1 frequency>...<allele 1 name> <allele N frequency>) |

Sets the "population" allele frequencies for a marker to be used by MCMC procedures that simulate missing genotypes for that marker. This currently only affects the set analysis and gpe commands. The obs option can fix the frequency to that observed for the currently active dataset.

Currently, only one marker at a time can have specified frequencies. To free the frequencies (allow calculation from the dataset), call the command without specifying any frequencies after the marker name.


>> include
>> gpe ldl
>> set freq ldl 0.999 0.001
>> gpe ldl

See also:

set analysis Enable inclusion of imputed alleles in GLM association analysis.
gpe Genotype probability estimates.
regress Generalized linear models.

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