MCGDTI

• Update(30/8/2017)
• PURPOSE:R package for the generalized disequilibrium test for association in qualitative traits incorporating genomic imprinting effects based on extended pedigrees. Pedigrees with missing genotypes are allowed and the Monte Carlo samples of the missing genotypes conditional on the observed genotypes will be used.
• NOTE: This package was built on R (version 3.4.1 with 32-bit). Users should install and use the package under the R (version 3.4.1 with 32-bit) environment. In addition, the results may be a little different for different runs when the pedigrees are incomplete due to the Monte Carlo sampling and estimation scheme.
• Complied R package file for Windows (in a zipped file): MCGDTI_1.0.zip
• Complied R package file for Linux and Unix (in a zipped, tar file): MCGDTI_1.0.tar.gz
• Instructions: Instructions.txt

References:

[1] Chen, W. M., Manichaikul, A., Rich, S. S. (2009). A generalized family-based association test for dichotomous traits. The American Journal of Human Genetics, 85(3):364-376.

[2] Ding, J., Lin, S., Liu, Y. (2006). Monte Carlo pedigree disequilibrium test for markers on the X chromosome. The American Journal of Human Genetics, 79(3):567-573.

[3] Ott, J., Lathrop, G. M. (1990). SLINK: a general simulation program for linkage analysis. The American Journal of Human Genetics, 47:A204.

[4] Li, J. L., Wang, P., Fung, W. K., Zhou, J. Y. (2017). Generalized disequilibrium test for association in qualitative traits incorporating imprinting effects based on extended pedigrees. (submitted)

[5] Zhou, J. Y., Ding, J., Fung, W. K., Lin, S. (2010). Detection of parent-of-origin effects using general pedigree data. Genetic Epidemiology, 34(2):151-158.