Likelihood ratio test to distinguish pleiotropy from linkage

assemble_Ve | Assemble into a matrix Ve from fit1_bvlmm() output |

assemble_Vg | Assemble into a matrix Vg from fit1_bvlmm() output |

calc_det_rss | Calculate determinants of cross-product of residuals matrices |

calc_ll_bvlmm | Calculate log-likelihood for a bivariate LMM |

calc_lod | Calculate LODs - two profile and one joint - for two traits |

calc_res | Calculate an array of residuals using Haley-Knott regression |

calc_rss | One-dimensional scan over a region of interest using only... |

calc_rss_one | Calculate RSS for a single locus and a single trait |

fit1_bvlmm | Fit a 2-locus, multivariate trait linear mixed effects model |

hk_residuals | Calculate residuals with Haley-Knott regression |

prep_pheno | Prepare phenotype for use with scan functions |

sim_pheno | Simulate phenotypes from genotype data |

sim_pheno2 | Simulate two phenotypes simultaneously |

sim_pheno_lmm | Simulate bivariate phenotype with incorporation of random... |

stagger_mats | Stagger two matrices of same size within a larger,... |

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