Description Usage Arguments Value Examples

mQTL mapping in bisulfite sequencing studies by fitting a binomial mixed model, incorporating allelic-specific methylation pattern.

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`geno` |
a data list containing the genotype data. |

`data` |
a data list containing the methylation data. |

`K` |
a known kinship matrix. This matrix should be a positive semi-definite matrix with dimensions equal to the samplie size. |

`Covariates` |
a matrix containing the covariates subject to adjustment (Default = NULL). |

`numCore` |
a positive integer specifying the number of cores for parallel computing (default = 1). |

`fit.maxiter` |
a positive integer specifying the maximum number of iterations when fitting the generalized linear mixed model (default = 500). |

`fit.maxiter` |
a positive number specifying tolerance, the difference threshold for parameter estimates below which iterations should be stopped (default = 1e-5). |

`loc` |
ordinal number of SNP-CpG pair being analyzed |

`numIDV` |
number of observations of SNP-CpG pair being analyzed |

`beta` |
the fixed effect parameter estimate for the predictor of interest. |

`se_beta` |
the standard deviation of fixed effect. |

`pvalue` |
P value for the fixed effect, based on the wald test. |

`h2` |
heritability of the transformed rate. |

`sigma2` |
total variance component. |

`converged` |
a logical indicator for convergence. |

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