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MCPDTI

  • Update (28/11/2014)
  • PURPOSE: R package for association analysis incorporating imprinting effects using general pedigree data for qualitative traits. 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 3.1.2 with 32-bit). Users should install and use the package under the R (version 3.1.2 with 32-bit) environment. In addition, this package calculates the P-value of MCPDTI based on R package “mvtnorm”. Therefore, before using the “MCPDTI” package, make sure that the R package “mvtnorm” has been installed and loaded into R.
  • Compiled R package file for Windows (in a zipped file): MCPDTI_1.0.zip
  • Sample pedigree file: ped.txt
  • Instructions: Instructions.txt

References:

[1] Ji-Yuan Zhou, Hai-Qiang He, Xiao-Ping You, Shao-Zhan Li, Ping-Yan Chen, Wing Kam Fung. 2014 A powerful association test for qualitative traits incorporating imprinting effects using general pedigree data. Journal of Human Genetics (accepted).

[2] Jie Ding, Shili Lin, Yang Liu. 2006 Monte Carlo pedigree disequilibrium test for markers on X chromosome. American Journal of Human Genetics, 79, 567-573.

[3] Eden R. Martin, Stephanie A. Monks, Liling L. Warren, Norman L. Kaplan. 2000 A test for linkage and association in general pedigrees: the pedigree disequilibrium test. American Journal of Human Genetics, 67, 146-154.

[4] Ji-Yuan Zhou, Jie Ding, Wing K. Fung, Shili Lin. 2010 Detection of parent-of-origin effects using general pedigree data. Genetic Epidemiology, 34, 151-158.