Mapping suscetibility loci in HZE irradiated HS/npt mice

get.effect.size | Effect size and odds ratio for SNP profiles |

get.effect.size.coxPH | Effect size and odds ratio for SNP profiles |

get.sig.thr | Given a set of maximum LOD scores, calculate the significance... |

GRconvert | Convert a Large list of data.frames into a GRangesList |

GRSD.assoc | Genome wide association mapping for binary phenotypes. |

GRSDassoc.perms | Permutation analysis for HZE. |

GRSDbinom | Association mapping on autosomal chromosomes with binary... |

GRSDbinom.fast | Association mapping on autosomal chromosomes with binary... |

GRSDbinom.permsfast | Association mapping on autosomal chromosomes with binary... |

GRSDbinom.regressGENO | Association mapping on autosomal chromosomes with binary... |

GRSDbinom.xchr | Association mapping on the X chromosome with binary variable... |

GRSDbinom.xchr.fast | Association mapping on the X chromosome with binary variable... |

GRSDbinom.xchr.permsfast | Association mapping on the X chromosome with binary variable... |

GRSDcoxph | Association mapping with survival outcomes using the CoxPH... |

GRSD.coxph | Genome wide association mapping using CoxPH |

GRSD.coxph4perms | Association mapping with survival outcomes using the CoxPH... |

GRSDcoxph.perms | Permutation analysis for CoxPH model in HZE. |

GRSDcoxph.xchr | Association mapping with survival outcomes using the CoxPH... |

GRSDcoxph.xchr4perms | Association mapping with survival outcomes using the CoxPH... |

GRSDpoisson | Association mapping on autosomal chromosomes with binary... |

GRSD.poisson | Genome wide association mapping with glm(family = poisson). |

GRSDpoisson.xchr | Association mapping on the X chromosome with poisson dist. |

HS.assoc.bootstrap | QTL Confidence Interval with Resample Model Averaging For... |

HS.cox.bootstrap | QTL Confidence Interval with Resample Model Averaging for Cox... |

loop.hs.qtl | Loop through to create a smaller file for heatmap input |

manhattan_plot | Allow for multiple, superimposed QTL plotting in mice.... |

maxLOD | Helper Function for QTL Support Intervals. |

multiplot | Allows for multiple plots (generated by ggplot2) |

plot.hs | Plot function (w/ binning to average markers and max LOD) |

plot.hs.color.qtl | Genome wide association plots with separate colors param... |

plot.hs.qtl | Convert function to average fixed regions and return LOD for... |

Scanone.assoc.perms | Permutation analysis for continuous traits in HZE ion exposed... |

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