Multiple Imputation for Proteomics

check.conditions | Check if the design is valid |

check.design | Check if the design is valid |

datasim | A single simulated dataset |

eBayes.mod | MI-aware Modifed eBayes Function |

formatLimmaResult | Format a Result from Limma |

hid.ebayes | MI-aware Modifed eBayes Function |

limmaCompleteTest.mod | Computes a hierarchical differential analysis |

make.contrast | Builds the contrast matrix |

make.design | Builds the design matrix |

make.design.1 | Builds the design matrix for designs of level 1 |

make.design.2 | Builds the design matrix for designs of level 2 |

make.design.3 | Builds the design matrix for designs of level 3 |

meanImp_emmeans | Multiple Imputation Estimate |

mi4limma | Differential analysis after multiple imputation |

mi4p-package | mi4p: Multiple imputation for proteomics |

mm_peptides | mm_peptides - peptide-level intensities for mouse |

multi.impute | Multiple imputation of quantitative proteomics datasets |

MVgen | Amputation of a dataset |

norm.200.m100.sd1.vs.m200.sd1.list | A list of simulated datasets. |

proj_matrix | Variance-Covariance Matrix Projection |

protdatasim | Data simulation function |

qData | Extract of the abundances of Exp1_R25_pept dataset |

rubin1.all | First Rubin rule (all peptides) |

rubin1.one | First Rubin rule (a given peptide) |

rubin2.all | Computes the 2nd Rubin's rule (all peptides) |

rubin2bt.all | 2nd Rubin's rule Between-Imputation component (all peptides) |

rubin2bt.one | 2nd Rubin's rule Between-Imputation Component (a given... |

rubin2wt.all | 2nd Rubin's rule Within-Variance Component (all peptides) |

rubin2wt.one | 2nd Rubin's rule Within-Variance Component (a given peptide) |

sTab | Experimental design for the Exp1_R25_pept dataset |

test.design | Check if xxxxxx |

within_variance_comp_emmeans | Multiple Imputation Within Variance Component |

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