Science-wise false discovery rate and proportion of true null hypotheses estimation

BMI_GIANT_GWAS_sample | Subset of SNPs from meta-analysis of BMI GWAS study. |

calculateSwfdr | Calculate the science-wise FDR (swfdr) |

check_class | check if an object is of a certain class |

check_df | validate degrees of freedom. |

check_lambda | validate lambda. They must be numeric, finite, sorted with... |

check_p | validate pvalues. They must be finite, in range [0,1] |

check_X | validate matrix of covariates. It must be compatible with a... |

compose.stats | Compose a two line report about a numeric vector |

compound.message | Compose and output a compound message and output |

fit_linear | Fit response values using a linear regression |

fit_logistic | Fit response values using a binomial/logit model |

get.components | Get a set intersection, but when second set is null default... |

get_number_decimals | Get number of decimals (i.e. return total number of digits... |

journals_pVals | P-values from abstracts from articles in 5 biomedical... |

lm_pi0 | Estimation of pi0, proportion of p-values consistent with a... |

lm_qvalue | Compute qvalues taking into account a matrix of covariates |

optimize.multiplier | recursive internal function to find an optimal value of... |

print.lm_pi0 | Display a summary of object lm_pi0 |

print.lm_qvalue | Display a summary of an lm_qvalue object |

regularize.interval | Force a set of values in a regular interval |

smooth.spline.pi0 | Fit smoothing splines to several curves |

summary.lm_pi0 | Display a summary of object lm_pi0 |

summary.lm_qvalue | Display a summary of object lm_qvalue |

unit.spline | Fit smoothing unit spline to one curve |

unit.spline.matrix | Construct a transformation matrix for a unit spline |

unit.spline.pi0 | Fit smoothing unit splines to several curves |

v2s | Helper to create a single string by concatenating items from... |

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