Description Usage Arguments Value Examples

aGE joint test

1 2 3 |

`Y` |
a numeric vector of phenotype values |

`G` |
a matrix or data frame for all RVs in the test gene or genomic region. The order of rows must match the order of Y. Missing is imputed as 0. |

`cov` |
a matrix or data frane with first column as the environmental variable to be tested. The order of rows must match the order of Y. |

`model` |
"binomial" for binary traits or "gaussian" for quantitative traits. |

`pow` |
Gamma set used to build a family of tests, default=c(1:6) for rare variants |

`n.perm` |
number of simulation to calculate the p-values, default=1000. Can increase to higher value depending on the signficiance level. |

`method` |
'Simulation': Monte Carlo Method |

`nonparaE` |
"T": use cubic splines for the environmental variable to fit the model; "F": use a linear function of the environmental variable to fit the model |

`DF` |
degree of freedom to use in the cubic splines, default=10. This option only works when nonparaE is set to "T". |

p-values

1 2 3 4 5 6 7 8 | ```
{
set.seed(12345)
phenotype <- c(rep(1,50),rep(0,50))
genotype <- data.frame(g1=sample(c(rep(1,10),rep(0,90))),g2=sample(c(rep(1,5), rep(0,95))))
covariates <- data.frame(Envir=rnorm(100), Age=rnorm(100,60,5))
exD <- list(Y=phenotype, G=genotype, X=covariates)
aGE.joint(Y=exD$Y, G=exD$G, cov=exD$X, model='binomial')
}
``` |

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