SWATH extended library generation and statistical data analysis

applyttest | Utility to apply a t-test to all rows of a matrix |

applyttestPep | Function to apply t-test separately for all peptides of each... |

buildSpectraLibPair | Build a spectra library by integrating a pair of spectrum... |

canonicalFormat | Standardise a sprectrum library data frame |

checkQuality | Checking for the integration quality of two libraries |

cleanLib | Spectrum library cleanining |

coverage | A function to calculate the coverage percentage |

cv | A function to calculate the CV (Coeffient of Variation) |

fdr.crit | A function to calculate the number of samples pass fdr... |

getFdrBins | Function to calculate the percentage of fdrs in each bin |

ionCorGS | Gold standard relative ion intensity correlation (spearman) |

medianNorm | Utility to median normalize a matrix by columns |

mlr | Function to implement mlr normalization |

mlrGroup | Function to do mlr normalization for a matrix group |

mlrrep | Function to do mlr normalizatiopn on a matrix of replicates |

outputLib | output a spectrum library into a PeakView format file |

plotAll | Plot statistical plots for two libraries |

plotDensities | Utility to do side by side density plots |

plotErrorBarsLines | Utility for clustering plots to plot lines and an overall... |

plotRelativeDensities | Plotting utility to overlay all relative densities |

plotRIICor | Plot relative ion intensity correlation of two libraries |

plotRTCor | Plot for retention time correlation of two libraries |

plotRTResd | Plot residuals for retention time prediction of two libraries |

quantification.accuracy | Measurment of quantification accuracy of two Swath results |

readLibFile | Load a spectrum library into a data frame |

reliabilityCheckLibrary | A function to check the coverage of the extended library... |

reliabilityCheckSwath | A function to check the coverage, fdr distrubtions,... |

swath.means | Computer Swath mean peak area for duplicated samples |

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