Statistical Analysis of High Throughput Proteomics Data

accum | Response calculation |

addIonSatistics | Summary statistics - Ion intensities per spectra |

addLoadings | Adjust for confounding - add an appropiate target |

addRetentionAtApex | Summary statistics - Calculates retention time statistics at... |

addRetentionIndexTimeStatistics | Summary statistics - Calculates index retention time... |

adjustBy | Adjust for confounding - Generic function for centring data |

adjusting | Adjust for confounding - State of the art adjustments for... |

adjustOne | Adjust for confounding - In one single experiment only |

avrgLoading | Adjust for confounding - calculates the average loading |

channelResponses | Response calculation |

copyLoadings | Adjust for confounding - copy loadings from one experiment to... |

factoring | Sample design - Generating multiple factor designs from... |

meetSelection | Data parsing - from Proteom Discover v1.4 |

mergeFrames | Merging multiple experiments |

norm2Reference | Response calculation |

pAction | Plotting p-value distributions |

plotMePeptide | Plot interaction plots of peptides |

plotMeProtein | Plot interaction plots of proteins |

pRetention | Plot Retention Time Statistics |

pVioline | Plot Retention Time Statistics in violine form |

pVolcano | Volcano plot |

responseStatisics | Summary statistics - Generic to calculate summary statistics |

selectByConfidence | Result filtering - Test for biological effect |

selectByEffect | Result filtering - Test for biological effect |

selectByFDR | Result filtering |

testForPeptideEffect | Data Analysis - Testing on peptide level |

testForProteinEffect | Data Analysis - Testing on protein level |

testing | Data Analysis - Testing features with Tukey Honest... |

testingOneshot | Data Analysis - Testing one feature without Tukey Honest... |

testingTukey | Data Analysis - Testing one feature with Tukey Honest... |

toAlpha | Measuring stability - angle of loading vector |

toProportions | Transformation - From intensity scales to density histrograms |

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