Family data in PLINK and MERLIN Sarah Medland
- Slides: 10
Family data in PLINK and MERLIN Sarah Medland
PLINK • Setting up the data • commands. txt
Caution. . . A single cluster For us this means only 1 type of relative No MZ twins + Sibs No parent-offspring trios
PLINK • within • Huber-White sandwich variance estimator
Huber-White sandwich variance estimator • general method for estimating the covariance matrix of parameter estimates. • • Huber, P. J. 1967. The behavior of maximum likelihood estimates under nonstandard conditions. In Proceedings of the Fifth Berkeley Symposium on Mathematical Statistics and Probability. Berkeley, CA: University of California Press, vol. 1, 221– 233. White, H. 1980. A heteroskedasticity-consistent covariance matrix estimator and a direct test for heteroskedasticity. Econometrica 48: 817– 830. • Yields asymptotically consistent covariance matrix estimates • without making distributional assumptions • and even if the assumed model underlying the parameter estimates is incorrect
Slight Technicality • Huber (1967) and White (1980), do not deal with clustering. Williams, R. L. 2000. A note on robust variance estimation for cluster-correlated data. Biometrics 56: 645– 646.
PLINK • qfam • between • within • total
Check out the results. . . Anything interesting?
MERLIN • Setting up the data • Running the score test • Running the LRT
HOW DO THE RESULTS COMPARE?
