Association testing with spatially structured phenotypes

choose_s0 | Select s0 using the method of Tusher, Tibshirani and Chu... |

dnase1_test_windows | Run a variety of tests in pre-defined windows |

find_segments | Use variance of smoothed permutation test statistics to... |

fret_rates | Calculate lambda and fdr for each peak |

fret_rates_prelim | Calculate per-base error rates for original and permutation... |

fret_stats | Calculate FRET test statistics |

get_stats | Helper function for calculating test statistics |

hello | Hello, World! |

ksmooth_0 | Box kernel smoother for integer positions |

ksmooth_0_cpp | Kernel smoother for integer locations |

ksmooth_0_stitch | Kernel smoother for integer locations |

maxes_1seg | Get peak heights and permuted peak heights for one segment |

stats_to_rates | Collect fret_stats temporary files |

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