The name is absent



36


Stata Technical Bulletin


STB-48


Hardy-Weinberg Equilibrium Test :

Pearson chi2 (1) = 1.956 Pr= 0.1620
likelihood-ratio chi2 (1) = 1.959 Pr= 0.1616
Exact significance prob = 0.1793

Example 2: multiallelic locus

Spencer et al. (1964) examined the distribution of the red cell acid phosphatase polymorphism in 178 randomly selected
individuals. They identified 3 alleles at this locus; A, B and C. We would like to test the null hypothesis that these data are
consistent with Hardy-Weinberg equilibrium. Their data has been entered into Stata. Here are the first ten observations:

. list in 1/10

alll       all2

1.

A

A

2.

A

B

3.

A

C

4.

B

B

5.

B

C

6.

A

B

7.

A

B

8.

B

B

9.

A

A

10.

B

B

We now perform the test for Hardy-Weinberg equilibrium:

. genhw alll all2

Genotype

I Observed

Expected (

Disequilibrium

Coefficient (D)

AA
AB

AC

BB
BC

CC

I          17

I          86

I              5

I          61

I              9

I              0

21.95

76.19

4.92

66.14

8.53

0.28

-0.0275

-0.0002

-0.0013

Total

Allele

I        178

I Observed

178.00

Frequency

Std. Err.

A
B

C

I        125

I        217

I          14

.+-----------

0.3511

0.6096

0.0393

0.0237

0.0242

0.0101

Hardy-Weinberg Equilibrium Test :

Pearson chi2 (3) =    3.078 Pr= 0.3798

likelihood-ratio chi2 (3) =    3.407 Pr= 0.3330

Similar to the output in the biallelic case, genotype and allele frequency tables are produced. However, instead of only one
disequilibrium coefficient, in the multiallelic case, a disequilibrium coefficient is estimated for each heterozygous genotype.

For these data, we fail to reject the null hypothesis that the population is in Hardy-Weinberg equilibrium with respect to
this locus.

Saved results

genhw saves in r():

Scalars

r(chi2)
r(df)
r(chi2_p)
r(lr.chi2)
r(lr_p)
r (p_exact )
r(D)


Pearson’s chi squared
degrees of freedom
significance probability (Pearson)
likelihood-ratio chi squared
significance probability (LR)
exact significance probability (biallelic only)
disequilibrium coefficient (biallelic only)



More intriguing information

1. On Social and Market Sanctions in Deterring non Compliance in Pollution Standards
2. The name is absent
3. Multi-Agent System Interaction in Integrated SCM
4. Altruism and fairness in a public pension system
5. The name is absent
6. The name is absent
7. The name is absent
8. Estimation of marginal abatement costs for undesirable outputs in India's power generation sector: An output distance function approach.
9. The open method of co-ordination: Some remarks regarding old-age security within an enlarged European Union
10. A Study of Prospective Ophthalmology Residents’ Career Perceptions