Authors Manon Martin (manon.martin@uclouvain.be) and Marie Tremblay-Franco (marie.tremblay-franco@inra.fr; Galaxy integration)
These steps correspond to the following steps in the PEPS-NMR R library (https://github.com/ManonMartin/PEPSNMR):
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 |
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.
Smoothing parameter lambda: The higher lambda is, the smoother the estimated solvent signal will be
The types of apodization are:
Zero Order Phase correction method:
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.
The searching window can be adapted:
shiftHandling: spectra can be shifted differently, we can handle misalignment of the left and right of the spectrum by different ways:
value of the reference peak: the value in ppm of the reference peak. By default the value is 0 ppm.
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.
Set negative intensities to zero: the set of negative intensities to zero is optional.
Version 3.3.0
Version 3.2.0
Version 3.1.0