Testing Pleiotropy in Multiparental Populations

add_pmap | Add physical map contents to tibble |

boot_pvl | Perform bootstrap sampling and calculate test statistics for... |

calc_Bhat | Calculate estimated allele effects, B matrix |

calc_covs | Calculate Vg and Ve from d-variate phenotype and kinship |

calc_invsqrt_mat | Calculate matrix inverse square root for a covariance matrix |

calc_lrt_tib | Calculate a likelihood ratio test statistic from the output... |

calc_profile_lods | Calculate profile lods for all traits |

calc_Sigma | Calculate the phenotypes covariance matrix Sigma |

calc_sqrt_mat | Calculate matrix square root for a covariance matrix |

check_identical | Check whether a vector, x, has all its entries equal to its... |

check_missingness | Check for missingness in phenotypes or covariates |

find_pleio_peak_tib | Find the marker index corresponding to the peak of the... |

fit1_pvl | Fit a model for a specified d-tuple of markers |

get_effects | Extract founder allele effects at a single marker from output... |

make_id2keep | Identify shared subject ids among all inputs: covariates,... |

pipe | Pipe operator |

plot_pvl | Plot tidied results of a pvl scan |

prep_mytab | Prepare mytab object for use within scan_pvl R code |

prep_X_list | Create a list of component X matrices for input to... |

qtl2pleio | qtl2pleio. |

rcpp_calc_Bhat | Estimate allele effects matrix, B hat, with Rcpp functions |

rcpp_calc_Bhat2 | Estimate allele effects matrix, B hat, with Rcpp functions |

rcpp_log_dmvnorm2 | Calculate log likelihood for a multivariate normal |

scan_pvl | Perform model fitting for all ordered pairs of markers in a... |

sim1 | Simulate a single data set consisting of n subjects and 2... |

subset_input | Subset an input object - allele probabilities array or... |

subset_kinship | Subset a kinship matrix to include only those subjects... |

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