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NMR_Preprocessing (version 3.3.0)
Group Delay Corrections
Group Delay Correction 0
Solvent Suppressions
Solvent Suppression 0
Apodizations
Apodization 0
Fourier Transforms
Fourier Transform 0
Zero Order Phase Corrections
Zero Order Phase Correction 0
Shift Referencings
Shift Referencing 0
Baseline Corrections
Baseline Correction 0
Negative intensities to Zeros
Negative intensities to Zero 0
Select 'YES' to display the spectra or 'NO' to not display them

Authors Manon Martin (manon.martin@uclouvain.be) and Marie Tremblay-Franco (marie.tremblay-franco@inra.fr; Galaxy integration)

Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.

Spectra preprocessing

Description

These steps correspond to the following steps in the PEPS-NMR R library (https://github.com/ManonMartin/PEPSNMR):

  • Group Delay suppression (First order phase correction)
  • Removal of solvent residuals signal from the FID
  • Apodization to increase the Signal-to-Noise ratio of the FID
  • Fourier transformation
  • Zero order phase correction
  • Shift referencing to calibrate the spectra with internal compound referencing
  • Baseline correction
  • Setting of negatives values to 0

Workflow position

Upstream tools

Name Output file Format
NMR_Read NMR_Read_dataMatrix Tabular
NMR_Read NMR_Read_sampleMetadata Tabular

Downstream tools

Name Output file Format
NMR_Alignement dataMatrix Tabular
NMR_Bucketing dataMatrix Tabular
Normalization dataMatrix Tabular
Univariate variableMetadata Tabular
Multivariate sampleMetadata Tabular
  variableMetadata Tabular

Input files

File Format
1 : dataMatrix tabular
2 : sampleMetadata tabular

dataMatrix file

sample x variable matrix with tabular separations and "." as decimal; the table must not contain metadata apart from row and column names; the row names must be identical to the rownames of the sample metadata.

sampleMetadata file

sample x metadata matrix with tabular separations and "." as decimal for numeric metadata and NA for missing values.

Steps parameters

Solvent Suppression

Smoothing parameter lambda: The higher lambda is, the smoother the estimated solvent signal will be

Apodization

The types of apodization are:

  • exp: The signal is multiplied by a decreasing exponential exp(-t/LineBroadening).
  • cos2: The signal is multiplied by the value of a cosinus squared from 0 (where its value is 1) until pi/2 (where its value is 0).
  • blockexp: The first part of the signal (described by the proportion of signal in the window) is left unchanged and the second is multiplied by exp(-t/LineBroadening) starting at value 1.
  • blockcos2: The first part is left unchanged as with blockexp and the second part is multiplied by a cosinus squared where its value starts at 1 at the end of the block and ends at 0 at the end of the signal.
  • gauss: The signal is multiplied by a gaussian window centered at the beginning of the FID and with sigma=1/LineBroadening.
  • hanning: The signal is multiplied by a hanning window : 0.5 + 0.5 cos.
  • hamming: The signal is multiplied by a hamming window : 0.54 + 0.46 cos.

Zero Order Phase Correction

Zero Order Phase correction method:

  • rms: A positiveness criterion is applied on the spectrum with a quantile probability parameter to trim the values.
  • max: Optimization of the maximal spectral intensity.

Exclusion area(s) for the Zero Order Phase Correction: enables to optimize the criterion with excluded spectral window(s), by default the water region is excluded.

Shift Referencing

The searching window can be adapted:

  • nearvalue: the search concentrates around the value of the reference peak in ppm.
  • all: search accross the whole ppm axis.
  • window: the search is operated in the windows defined by the Search_zone bounds.

shiftHandling: spectra can be shifted differently, we can handle misalignment of the left and right of the spectrum by different ways:

  • zerofilling: The extremities at which a spectrum is not defined are replaced by 0. It makes sense since in practice the spectrum is close to zero at the extremities.
  • NAfilling: The extremities at which a spectrum is not defined are replaced by NA.
  • circular: The spectra are shifted circularly which means that the end of a spectrum is reproduced at the beginning.
  • cut: The ppm values for which some spectra are not defined are removed.

value of the reference peak: the value in ppm of the reference peak. By default the value is 0 ppm.

Baseline Correction

Smoothing parameter: the larger it is, the smoother the estimated baseline will be.

Asymmetry parameter: the smaller it is, the less the estimated baseline will try to follow peaks when it is under the spectrum and the more it will try to be under the spectrum.

numerical precision: numerical precision for convergence when estimating the baseline.

Exclusion area(s) for the Baseline Correction: enables to optimize the criterion with excluded spectral window(s), by default the water region is excluded.

Negative intensities to Zero

Set negative intensities to zero: the set of negative intensities to zero is optional.

Output files

NMR_Preprocessing_dataMatrix
tabular output
Data matrix with n rows (descriptors) and p columns (samples) containing the preprocessed spectra.

NMR_Preprocessing_variableMetadata
tabular output
Data matrix with 1 row (ppm value) and p columns (descriptors).

NMR_Preprocessing_log
text output
Contains warnings and the input parameters

NMR_Preprocessing_graph.pdf
pdf output
line plots of preprocessed spectra


Changelog/News

Version 3.3.0

  • Debugged R scripts for possibly negative baselines

Version 3.2.0

  • Updated R scripts and the help section of NMR_ReadFids and NMR_preprocessing
  • Added sections
  • Created a variableMetadata file in output of the NMR_preprocessing module
  • Homogenised the input-output file names with the other modules
  • Suppressed the option ptw for the baseline correction, set to TRUE all the time now
  • Shift referencing: other values than 0 are admitted
  • The log file recovers the input/output parameters
  • Added an exclusion zone for the computation of the Baseline Correction criterion
  • Switched Internal Referencing (goes second) and Zero Order Phase Correction (goes first)

Version 3.1.0

  • Implementation of NMR_ReadFids and NMR_preprocessing