| Title: | Datasets for the PepsNMR package |
|---|---|
| Description: | This package contains all the datasets used in the PepsNMR package. |
| Authors: | Manon Martin [aut, cre], Bernadette Govaerts [aut, ths], Pascal de Tullio [dtc] |
| Maintainer: | Manon Martin <[email protected]> |
| License: | GPL-2 | file LICENSE |
| Version: | 1.31.0 |
| Built: | 2026-10-14 11:44:53 UTC |
| Source: | https://github.com/bioc/PepsNMRData |
PepsNMR package
This package provides RData and Bruker files of raw and (partially) pre-processed metabolomic 1H NMR datasets from human urine and serum.
The raw Bruker files of the Human Serum are stored in the extdata
directory of this package. They are refered as the RawFidData_HS
dataset.
The (partially) pre-processed metabolomic 1H NMR datasets are in the form
of RData files with the following elements:
Data_HS_sp4 first FIDs and spectra of the Human Serum database after each preprocessing step.
Data_HU_sp4 first FIDs and spectra of the Human Urine database after each preprocessing step.
FidData_HSMatrix containing the raw Free Induction Decays of the Human Serum database.
FidData_HUMatrix containing the raw Free Indiction Decays of the Human Urine database.
FidInfo_HS_spMatrix containing acquisition parameters for the 4 first Human Serum FIDs.
FidInfo_HSMatrix containing acquisition parameters of the Human Serum FIDs.
FidInfo_HU_spMatrix containing acquisition parameters for the 4 first Human Urine FIDs.
FidInfo_HUMatrix containing acquisition parameters of the Human Urine FIDs.
FinalSpectra_HSMatrix containing the Human Serum spectra after the full pre-treatment process.
FinalSpectra_HUMatrix containing the Human Urine spectra after the full pre-treatment process.
Group_HSProvides the group (1|2|3|4) to which belongs each signal/spectrum of the Human Serum database.
Group_HUProvides the group (1/2/3) to which belongs each signal/spectrum of the Human Urine database.
RawFidData_HSRaw Bruker files for the Human Serum datase t.
| Package: | PepsNMRData |
| Type: | Package |
| Version: | 0.99.0 |
| License: | GPLv2 |
2 different datasets are provided: Human Urine and Human Serum 1H NMR
Benoît Legat, Bernadette Govaerts & Manon Martin
Maintainer: Manon Martin <[email protected]>
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).
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.
# RData file data("Data_HS_sp") # Raw Bruker file path <- system.file("extdata", package = "PepsNMRData") list.files(path) list.dirs(path, full.names = FALSE)# RData file data("Data_HS_sp") # Raw Bruker file path <- system.file("extdata", package = "PepsNMRData") list.files(path) list.dirs(path, full.names = FALSE)
4 first FIDs and spectra of the Human Serum database after
each preprocessing step.
For more details on this database, use help(FidData_HS).
data("Data_HS_sp")data("Data_HS_sp")
A list with 14 objects that are complex matrices. 4 observations/object:
FidData_HS_0Raw FIDs.
FidData_HS_1FIDs after first order phase correction.
FidData_HS_2FIDs after solvent residuals suppression.
FidData_HS_3FIDs after apodization.
Spectrum_data_HS_4Spectra after fourier transformation.
Spectrum_data_HS_5Spectra after zero order phase correction.
Spectrum_data_HS_6Spectra after internal calibration.
Spectrum_data_HS_7Spectra after baseline correction.
Spectrum_data_HS_8Spectra after negative values zeroing.
Spectrum_data_HS_9Spectra after warping.
Spectrum_data_HS_10Spectra after window selection.
Spectrum_data_HS_11Spectra after bucketing.
Spectrum_data_HS_12Spectra after region removal.
Spectrum_data_HS_13Spectra after normalization.
Data provided by Dr. Pascal de Tullio and coworkers of the Pharmaceutical Chemistry Laboratory in the Pharmacy Department of the University of Liege (ULg), Belgium.
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).
plot(Re(Data_HS_sp$FidData_HS_0[1,]), type="l")plot(Re(Data_HS_sp$FidData_HS_0[1,]), type="l")
4 first FIDs and spectra of the Human Urine database after
each preprocessing step.
For more details on this database, use help(FidData_HU).
data("Data_HU_sp")data("Data_HU_sp")
A list with 15 objects that are complex matrices with 4 observations/object:
FidData_HU_0Raw FIDs.
FidData_HU_1FIDs after first order phase correction.
FidData_HU_2FIDs after solvent residuals suppression.
FidData_HU_3FIDs after apodization.
Spectrum_data_HU_4Spectra after fourier transformation.
Spectrum_data_HU_6Spectra after zero order phase correction.
Spectrum_data_HU_5Spectra after internal calibration.
Spectrum_data_HU_7Spectra after baseline correction.
Spectrum_data_HU_8Spectra after negative values zeroing.
Spectrum_data_HU_9Spectra after warping.
Spectrum_data_HU_10Spectra after window selection.
Spectrum_data_HU_11Spectra after bucketing
Spectrum_data_HU_12Spectra after region removal.
Spectrum_data_HU_13Spectra after zone aggregation for the citrate peak.
Spectrum_data_HU_14Spectra after normalization.
Data provided by Dr. Pascal de Tullio and coworkers of the Pharmaceutical Chemistry Laboratory in the Pharmacy Department of the University of Liege (ULg), Belgium.
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).
plot(Re(Data_HU_sp$FidData_HU_0[1,]), type="l")plot(Re(Data_HU_sp$FidData_HU_0[1,]), type="l")
Matrix containing the raw Free Induction Decays of the Human
Serum database.
The experimental design is as follow: serum was collected from 4 blood donors
(their class membership is available in Group_HS). Measurements were
performed on 8 different days with replicates. The order of the measurements
were permuted according to a latin hypercube sampling method.
data("FidData_HS")data("FidData_HS")
A complex matrix of 32 spectra with 32768 time points.
Data provided by Dr. Pascal de Tullio and coworkers of the Pharmaceutical Chemistry Laboratory in the Pharmacy Department of the University of Liege (ULg), Belgium.
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).
See also FidInfo_HS for acquisition parameters and
Group_HS for the class of FID samples.
data(FidData_HS) plot(Re(FidData_HS[1,]), type = "l")data(FidData_HS) plot(Re(FidData_HS[1,]), type = "l")
Matrix containing the raw Free Indiction Decays of the Human
Urine database. The experimental design is as follow: urine was collected
from 3 donors (their class membership is available in Group_HU).
data("FidData_HU")data("FidData_HU")
A complex matrix of 24 spectra with 29411 time points.
Data provided by Dr. Pascal de Tullio and coworkers of the Pharmaceutical Chemistry Laboratory in the Pharmacy Department of the University of Liege (ULg), Belgium.
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).
See also FidInfo_HU for acquisition parameters and
Group_HU for the class of FID samples.
data(FidData_HU) plot(Re(FidData_HU[1,]), type = "l")data(FidData_HU) plot(Re(FidData_HU[1,]), type = "l")
Matrix containing acquisition parameters of the Human Serum FIDs.
data("FidInfo_HS")data("FidInfo_HS")
A matrix with 32 observations and 9 variables:
Time domain size
Determine the endiness of stored data. If 0 -> Little Endian; if 1 -> Big Endian
Digitization mode
Decimation rate of digital filter
DSP firmware version
Sweep width in Hz
Sweep width in ppm
Spectrometer frequency offset
Dwell time in microseconds
Data provided by Dr. Pascal de Tullio and coworkers of the Pharmaceutical Chemistry Laboratory in the Pharmacy Department of the University of Liege (ULg), Belgium.
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).
See also FidData_HS for the FIDs and Group_HS
for the class membership of FID samples.
data(FidInfo_HS)data(FidInfo_HS)
Matrix containing acquisition parameters for the 4 first Human Serum FIDs.
data("FidInfo_HS_sp")data("FidInfo_HS_sp")
A matrix with 4 observations and 9 variables.
Variables are:
Time domain size
The endiness of stored data. If 0 -> Little Endian; if 1 -> Big Endian
Digitization mode
Decimation rate of digital filter
DSP firmware version
Sweep width in Hz
Sweep width in ppm
Spectrometer frequency offset
Dwell time in microseconds
Data provided by Dr. Pascal de Tullio and coworkers of the Pharmaceutical Chemistry Laboratory in the Pharmacy Department of the University of Liege (ULg), Belgium.
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).
See also Data_HS_sp for the FIDs.
data(FidInfo_HS)data(FidInfo_HS)
Matrix containing acquisition parameters of the Human Urine FIDs.
data("FidInfo_HU")data("FidInfo_HU")
A matrix with 24 observations and 10 variables:
Time domain size
Determine the endiness of stored data. If 0 -> Little Endian; if 1 -> Big Endian
Digitization mode
Decimation rate of digital filter
DSP firmware version
Sweep width in Hz
Sweep width in ppm
Spectrometer frequency offset
Group Delay
Dwell time in microseconds
Data provided by Dr. Pascal de Tullio and coworkers of the Pharmaceutical Chemistry Laboratory in the Pharmacy Department of the University of Liege (ULg), Belgium.
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).
See also FidData_HU for the FIDs and Group_HU
for the class membership of FID samples.
data(FidInfo_HU)data(FidInfo_HU)
Matrix containing acquisition parameters for the 4 first Human Urine FIDs.
data("FidInfo_HU_sp")data("FidInfo_HU_sp")
A matrix with 4 observations and 10 variables.
Variables are:
Time domain size
The endiness of stored data. If 0 -> Little Endian; if 1 -> Big Endian
Digitization mode
Decimation rate of digital filter
DSP firmware version
Sweep width in Hz
Sweep width in ppm
Spectrometer frequency offset
Group Delay
Dwell time in microseconds
Data provided by Dr. Pascal de Tullio and coworkers of the Pharmaceutical Chemistry Laboratory in the Pharmacy Department of the University of Liege (ULg), Belgium.
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).
See also Data_HU_sp for the FIDs.
data(FidInfo_HU)data(FidInfo_HU)
Matrix containing the Human Serum spectra after the full
pre-treatment process. At this stage the spectra are fully pre-processed.
For more details on this database, see help(FidData_HS).
data("FinalSpectra_HS")data("FinalSpectra_HS")
A complex matrix with 32 observations and 500 frequency data points in a ppm scale.
Data provided by Dr. Pascal de Tullio and coworkers of the Pharmaceutical Chemistry Laboratory in the Pharmacy Department of the University of Liege (ULg), Belgium.
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).
See also FidData_HS for the raw FIDs and Group_HS
for the samples class.
data(FinalSpectra_HS) plot(Re(FinalSpectra_HS[1,]), type="l")data(FinalSpectra_HS) plot(Re(FinalSpectra_HS[1,]), type="l")
Matrix containing the Human Urine spectra after the full pre-treatment process. At this stage the spectra are fully pre-processed.
data("FinalSpectra_HU")data("FinalSpectra_HU")
A complex matrix with 24 observations and 500 frequency data points in a ppm scale.
Data provided by Dr. Pascal de Tullio and coworkers of the Pharmaceutical Chemistry Laboratory in the Pharmacy Department of the University of Liege (ULg), Belgium.
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).
See also FidData_HU for the raw FIDs and Group_HU
for the samples class.
data(FinalSpectra_HU) plot(Re(FinalSpectra_HU[1,]), type="l")data(FinalSpectra_HU) plot(Re(FinalSpectra_HU[1,]), type="l")
Provides the group (1|2|3|4) to which belongs each signal/spectrum
of the Human Serum database. For more details on this database,
see help(FidData_HS).
data("Group_HS")data("Group_HS")
A vector of length 32.
Data provided by Dr. Pascal de Tullio and coworkers of the Pharmaceutical Chemistry Laboratory in the Pharmacy Department of the University of Liege (ULg), Belgium.
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).
See also FidInfo_HS for acquisition parameters and
FidData_HS for the FIDs.
data(Group_HS)data(Group_HS)
Provides the group (1/2/3) to which belongs each signal/spectrum of the Human Urine database.
data("Group_HU")data("Group_HU")
A vector of length 24.
Data provided by Dr. Pascal de Tullio and coworkers of the Pharmaceutical Chemistry Laboratory in the Pharmacy Department of the University of Liege (ULg), Belgium.
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).
See also FidInfo_HU for acquisition parameters and
FidData_HU for the FIDs.
data(Group_HU)data(Group_HU)
Contains the Bruker files for the 32 spectra of the Human Serum dataset.
data("RawFidData_HS")data("RawFidData_HS")
The inst/extdata directory contains a series of sub-directories, one by FID.
Data provided by Dr. Pascal de Tullio and coworkers of the Pharmaceutical Chemistry Laboratory in the Pharmacy Department of the University of Liege (ULg), Belgium.
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.
# Raw Bruker file path <- system.file("extdata", package = "PepsNMRData") list.files(path) list.dirs(path, full.names = FALSE)# Raw Bruker file path <- system.file("extdata", package = "PepsNMRData") list.files(path) list.dirs(path, full.names = FALSE)