Function reference • metabom8

Import 1D NMR data
`read1d()` `read1d_proc()`	Import 1D NMR spectra
`read1d_raw()`	Read-in 1D NMR FIDs and process to spectra
Visualising spectra
`matspec()`	Plot overlayed NMR spectra
`spec()`	Plot single NMR spectrum
`specOverlay()`	Higher level plotting function to overlay NMR spectra (ggplot2 based)
Pre-processing and quality control
`alignSegment()`	Align an NMR spectra to a reference spectrum (cross-correlation)
`binning()`	Spectral data binning
`bline()` `bcor()`	Baseline correction for 1D NMR spectra
`calibrate()`	Chemical shift calibration
`excise1d()`	Excise standard chemical shift regions
`get.idx()` `get_idx()`	Select indices of the chemical shift array taht corresponding to a chemical shift region
`lw()`	Full width at half-maximum (fwhm)
`noise.est()`	Estimation of noise level of 1D spectrum
`normErectic()`	Normalise by the ERETIC signal
`pqn()`	Probabilistic quotient normalisation
Scalings, effect size
`es_cdelta()`	Cliff's delta (effect size)
`minmax()`	Min-max scaling
`scRange()`	Range scaling
PCA and O-PLS modelling and model interpretation
`cvanova()`	Cross-validated ANOVA for O-PLS models
`dmodx()`	Calculating distance to the model in X space
`eruption()`	Eruption plot for OPLS-DA model visualisation
`opls()`	Orthogonal-Partial Least Squares (O-PLS)
`opls_perm()`	OPLS model Y-permutations
`pca()`	Principal Component Analysis
`ppick()`	Find local extrema in NMR spectra (peak picking)
`plotload()`	Visualising PCA or OPLS loadings for NMR data
`plotload_cat()`	Plot PCA or O-PLS loadings
`plotscores()`	Plotting PCA or OPLS model scores
`predict_opls()`	OPLS model predictions
`specload()`	Overlay PCA or OPLS loadings with spectra
Metabolite ID-ing
`stocsy()`	Statistical Total Correlation Spectroscopy (STOCSY)
`storm()`	Subset Optimisation by Reference Matching (STORM)
`plotStocsy()`	Plot Statistical Total Correlation Spectroscopy (STOCSY)
Class definitions
`OPLS_metabom8-class`	An S4 class to represent an OPLS model constructed with metabom8
`PCA_metabom8-class`	An S4 class to represent an PCA model constructed with metabom8
`stocsy1d_metabom8-class`	An S4 class to represent STOCSY model constructed with metabom8

Reference

Import 1D NMR data

Visualising spectra

Pre-processing and quality control

Scalings, effect size

PCA and O-PLS modelling and model interpretation

Metabolite ID-ing

Class definitions