OR_tilde.R

OR_tilde.R is an R program that computes the corrected odds ratio (OR) for the association between genetic variants and secondary phenotype, where secondary phenotype is associated with primary disease in the original study.

Version 1.3 of OR_tilde is a new release to the public.

The major changes include (Wang and Shete, Ann Hum Genet, 2012):

• Allow the secondary phenotype and genetic variant have an interactive effect on the primary disease

• Use Wald test to evaluate the p value for OR_tilde based on asymptotic standard error

• Modify the bootstrapping procedure for empirical p value

The program and sample files:

• • README.txt: a description of how to run OR_tilde.R, input file formats and examples of input and output files

  • OR_tilde.R : R program for computing OR_tilde

  • OR_fun: the function file for constructing three nonlinear equations, and will be called in program OR_tilde.R

  • st_fun: the function file for constructing three nonlinear equations, and will be called in program OR_tilde.R

  • boot_fun: the function file for constructing three nonlinear equations, and will be called in program OR_tilde.R

  • parameter: a sample input parameter file

  • parameter_add: a sample input parameter file

  • initial: a sample input file for initial values used in solving the nonlinear equations

  • OR_tilde.out: a sample outcome file

Version 1.1 of OR_tilde was the initial release to the public.

• • README.txt: a description of how to run OR_tilde.R, input file formats and examples of input and output files

  • OR_tilde.R : R program for computing OR_tilde

  • OR_fun: the function file for constructing three nonlinear equations, and will be called in program OR_tilde.R

  • parameter: a sample input parameter file

  • initial: a sample input file for initial values used in solving the nonlinear equations

  • OR_tilde.out: a sample outcome file

Reference:

Wang J, Shete S. Estimation of odds ratios of genetic variants for the secondary phenotypes associated with primary diseases. Genet Epidemiol 35(3):190-200, 4/2011. e-Pub 2/2011.

Wang J, Shete S. Analysis of secondary phenotype involving the interactive effect of the secondary phenotype and genetic variants on the primary disease. Ann Hum Genet 76(6):484-99, 11/2012. e-Pub 8/2012.