18
Stata Technical Bulletin
STB-57
Options
label(genotypes) requests that labels are used in the output of the genotype frequency table.
binvar requests that the standard errors from a binomial distribution are reported for each allele frequency. These standard
errors are calculated under the assumption that the population is under HWE. By default, standard errors that do not require
this assumption are reported.
Remarks
genhwcci performs asymptotic tests for HWE for genotypic counts of cases given the controls are under HWE. It also
estimates the disequilibrium coefficient (D) and its standard error for genotypic counts of cases and controls, separately. See
Methods and formulas for details.
Example
Helzlsouer et al. 1998 conducted a case-control study for the association of CYP17 polymorphism and breast cancer, in
which 109 cases and 113 controls were collected. We test the hypotheses whether the cases and controls are under HWE, separately.
Given the controls are under HWE, we test whether the cases are under HWE. An immediate command is used for testing the
HWE.
. genhwcci 41 47 21 37 58 18, label(AA AB BB)
Genotype ∣ Case Control ∣ Total
------------+-------------------------------+-------------
AA I 41 37 I 78
AB I 47 58 I 105
BB I 21 18 I 39
------------+-------------------------------+-------------
total I 109 113 I 222
Case
|
Allele ∣ Case |
Frequency |
Std. Err. | |
|
A I 129 B I 89 |
0.5917 0.4083 |
0.0350 0.0350 | |
|
————————————⅛-——————————— total I 218 |
1.0000 |
— | |
|
Estimated disequilibrium coefficient Hardy-Weinberg Equilibrium Test : Pearson chi2 (1) = 1.261 Control Allele ∣ Control Frequency |
(D) = SE = Pr= |
= 0.0260 = 0.0232 0.2614 0.2620 0.3204 Std. Err. | |
|
A I 132 B I 94 |
0.5841 0.4159 |
— 0.0318 0.0318 | |
|
——————————+—----------- total I 226 |
1.0000 |
— | |
|
Estimated disequilibrium coefficient (D) = SE = Hardy-Weinberg Equilibrium Test : Pearson chi2 (1) = 0.360 Pr= Test HO: cases under HWE: (given controls |
= -0.0137 = 0.0227 0.5487 0.5481 0.6983 under HWE) | ||
The label () option is used to label the genotypes in the table. The order of the genotypes is in the same order as given in the
syntax.
For this example, there is no significant evidence that the genotypic counts of cases and controls are not under HWE. Even
given the controls are under HWE, there is still no significant evidence that the cases are not under HWE.