Sib-pair Command: set frequencies

Class	Analysis and data manipulation command
Name	set frequencies
Arguments	<marker> [(<allele 1 frequency>...<allele N frequency>) | (<allele 1 name> <allele 1 frequency>...<allele 1 name> <allele N frequency>) | observed]

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.

Example:

>> include williamsex.in
>> 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.