Description Usage Arguments Details Value Author(s) References Examples

View source: R/ZeroOrderPhaseCorrection.R

The function corrects the spectra in order to have their real part in an absorptive mode.

1 2 3 4 |

`Spectrum_data` |
Matrix containing the spectra in ppm, one row per spectrum. |

`type.zopc` |
Method used to select the angles to rotate the spectra. See details. |

`plot_rms` |
Contains a vector of row names for which a debug plot should be made showing the value of the function we try to minimize as a function of the phase. |

`returnAngle` |
If |

`createWindow` |
If |

`angle` |
If not |

`plot_spectra` |
If |

`ppm.zopc` |
If |

`exclude.zopc` |
If not |

`verbose` |
If |

We focus our optimization on the positiveness of the real part which should be in an absoptive mode.

When `type.zopc`

is `"rms"`

, a positiveness criterion is measured for each spectrum. `"manual"`

is used when a vector of angles are specified in `angle`

and `"max"`

will optimize the maximum spectral intensity in the non-excluded window(s). Beware that if `exclude.zopc`

is not `NULL`

, the optimization will only consider the non-excluded spectral window(s).

By default the water region (5.1 - 4.5) is ignored.

`BaselineCorrection`

and `NegativeValuesZeroing`

will take care of the last negative values of the real part of the spectra. See the reference for more details.

`Spectrum_data` |
The matrix of rotated spectra. |

Benoît Legat & Manon Martin

Martin, M., Legat, B., Leenders, J., Vanwinsberghe, J., Rousseau, R., Boulanger, B., & Govaerts, B. (2018). PepsNMR for 1H NMR metabolomic data pre-processing. *Analytica chimica acta*, 1019, 1-13.

Rousseau, R. (2011). *Statistical contribution to the analysis of metabonomics data in 1H NMR spectroscopy*
(Doctoral dissertation, PhD thesis. Institut de statistique, biostatistique et sciences actuarielles, Université catholique de Louvain, Belgium).

1 2 3 | ```
require(PepsNMRData)
Zopc.res <- ZeroOrderPhaseCorrection(Data_HS_sp$Spectrum_data_HS_4,
ppm.zopc = FALSE, exclude.zopc = list(c(5000,15000)))
``` |

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