Package: metabom8 1.0.8

Torben Kimhofer

metabom8: A High-Performance R Package for Metabolomics Modeling and Analysis

Tools for 1D NMR metabolomics workflows, including import and preprocessing of Bruker experiments, multivariate modeling (PCA, PLS, OPLS) and model analytics and validation (y-permutations, cv-anova). Performance-critical routines are implemented in C++ and use the Armadillo and Eigen linear algebra libraries to improve runtime.

Authors:Torben Kimhofer [aut, cre]

metabom8_1.0.8.tar.gz
metabom8_1.0.8.zip(r-4.7-x86_64)metabom8_1.0.8.zip(r-4.7-arm64)metabom8_1.0.8.zip(r-4.6-x86_64)metabom8_1.0.8.zip(r-4.6-arm64)metabom8_1.0.8.zip(r-4.5-x86_64)
metabom8_1.0.8.tgz(r-4.6-x86_64)metabom8_1.0.8.tgz(r-4.6-arm64)metabom8_1.0.8.tgz(r-4.5-x86_64)metabom8_1.0.8.tgz(r-4.5-arm64)
metabom8_1.0.8.tar.gz(r-4.7-arm64)metabom8_1.0.8.tar.gz(r-4.7-x86_64)metabom8_1.0.8.tar.gz(r-4.6-arm64)metabom8_1.0.8.tar.gz(r-4.6-x86_64)
metabom8_1.0.8.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
metabom8/json (API)

# Install 'metabom8' in R:

install.packages('metabom8', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/tkimhofer/metabom8/issues

Pkgdown/docs site:https://tkimhofer.github.io

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

covid - COVID-19 blood plasma proton NMR spectra
covid_raw - COVID-19 blood plasma proton NMR spectra
hiit_raw - High-intensity interval training (HIIT) 1H NMR urine dataset

On BioConductor:metabom8-1.1.7(bioc 3.24)metabom8-1.0.8(bioc 3.23)

metabolomics cheminformatics preprocessing dataimport alignment workflowstep armadillo eigen rcpp cpp

5.91 score 4 stars 15 scripts 357 downloads 58 exports 84 dependencies

Last updated from:8a7265b57b (on RELEASE_3_23). Checks:14 NOTE, 2 OK. Indexed: no.

Target	Result	Time
bioc-checks	NOTE	196
linux-devel-arm64	NOTE	242
linux-devel-x86_64	NOTE	335
source / vignettes	OK	267
linux-release-arm64	NOTE	239
linux-release-x86_64	NOTE	329
macos-release-arm64	NOTE	210
macos-release-x86_64	NOTE	430
macos-oldrel-arm64	NOTE	170
macos-oldrel-x86_64	NOTE	431
windows-devel-arm64	NOTE	369
windows-devel-x86_64	NOTE	316
windows-release-arm64	NOTE	318
windows-release-x86_64	NOTE	282
windows-oldrel-x86_64	NOTE	291
wasm-release	OK	145

Exports:add_note align_segment align_spectra balanced_boot balanced_mc binning bline calibrate cliffs_d correct_baseline correct_lw cv_anova dmodx ellipse2d es_cdelta excise fitted get_idx get_provenance get.idx hotellingsT2 kfold list_preprocessing loadings lw matspec mc minmax noise_sd norm_eretic opls pareto_scaling pca plot_spec plotStocsy pls ppick ppick2 pqn prep_X print_preprocessing print_provenance read1d read1d_proc read1d_raw scores scRange show spec stocsy storm stratified_kfold summary unscaled uv_scaling vip weights xres

Dependencies:abind askpass base64enc Biobase BiocGenerics bslib cachem cli colorRamps cpp11 crayon crosstalk curl data.table digest dplyr ellipse evaluate farver fastmap fontawesome fs generics ggplot2 ggrepel glue gtable highr hms htmltools htmlwidgets httr isoband jquerylib jsonlite knitr labeling later lazyeval lifecycle magrittr MASS memoise mime openssl otel pcaMethods pillar pkgconfig plotly plyr prettyunits pROC progress promises ptw purrr R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppDE RcppEigen reshape2 rlang rmarkdown S7 sass scales signal stringi stringr sys tibble tidyr tidyselect tinytex utf8 vctrs viridisLite withr xfun yaml

Getting Started

Rendered fromgetting-started.Rmdusingknitr::rmarkdown

Last update: 2026-05-10
Started: 2026-03-06

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Permutation-test summary from an opls_perm out_df table	.perm_test_from_table
Add user note to metabom8 provenance Appends a user annotation to the '"m8_prep"' attribute. The step title is formatted as '"note {username}"'. The timestamp is stored in 'params', and the user message is stored in 'notes'.	add_note
Align NMR Spectra in a Selected Shift Region	align_segment
Cohort-Guided Interval Alignment for 1D NMR Spectra	align_spectra
Balanced bootstrap resampling strategy	balanced_boot
Balanced Monte-Carlo resampling strategy	balanced_mc
Spectral data binning	binning
Chemical Shift Calibration	calibrate
Cliff's Delta Effect Size	cliffs_d es_cdelta
Baseline Correction for Spectral Data	bline correct_baseline
Linewidth correction by scaling spectra to a reference linewidth	correct_lw
COVID-19 blood plasma proton NMR spectra (processed)	covid
COVID-19 blood plasma proton NMR spectra (raw)	covid_raw
Cross-validated ANOVA for O-PLS models	cv_anova
Distance to the Model in X-Space (DModX)	dmodx
Calculate 2D Hotelling T^2 Ellipse	ellipse2d
Excise Chemical Shift Regions from 1D NMR Spectra	excise
Extract fitted Y values	fitted fitted,m8_model-method
Select Indices for a Chemical Shift Region	get.idx get_idx
Retrieve metabom8 provenance metadata	get_provenance
High-intensity interval training (HIIT) 1H NMR urine dataset	hiit_raw
Hotelling T^2 Statistic	hotellingsT2
K-fold cross-validation strategy	kfold
List available preprocessing steps	list_preprocessing
Model loadings	loadings,m8_model-method
Full Width at Half Maximum (FWHM) Estimation	lw
m8_model class Model object returned by 'pca()', 'pls()', and 'opls()'.	m8_model m8_model-class show,m8_model-method summary,m8_model-method
Monte-Carlo cross-validation strategy	mc
metabom8: A High-Performance R Package for Metabolomics Modeling and Analysis	metabom8-package metabom8
Min-Max Scaling to [0,1]	minmax
Estimate Noise Standard Deviation in 1D NMR Spectra	noise_sd
Normalise Spectra Using ERETIC Signal	norm_eretic
Fit an Orthogonal Partial Least Squares (O-PLS) model	opls
OPLS Model Validation via Y-Permutation	opls_perm
Pareto Scaling Leaves variables unscaled. Optional centering.	pareto_scaling
Principal Component Analysis (PCA)	pca
Plot 1D NMR Spectra	matspec plot_spec spec
Plot STOCSY result	plotStocsy
Fit a Partial Least Squares (PLS) model	pls
Find Local Extrema in NMR Spectra (Peak Picking)	ppick
Peak picking using Savitzky–Golay derivatives	ppick2
Probabilistic Quotient Normalisation (PQN)	pqn
Applies a preprocessing strategy to a numeric matrix.	prep_X
List available preprocessing functions Returns the preprocessing utilities provided by 'metabom8'.	print_preprocessing
Print metabom8 preprocessing pipeline	print_provenance
Import 1D NMR spectra (TopSpin processed)	read1d read1d_proc
Read raw FIDs and process to spectra	read1d_raw
PLS/OPLS model scores	scores scores,m8_model-method
Min-Max Scaling to Arbitrary Range	scRange
Statistical Total Correlation Spectroscopy (STOCSY)	stocsy
Subset Optimisation by Reference Matching (STORM)	storm
Y-stratified k-fold cross-validation strategy	stratified_kfold
No Scaling This function defines a preprocessing strategy that is applied via 'prep_X'.	unscaled
Unit Variance Scaling This function defines a preprocessing strategy that is applied via 'prep_X'.	uv_scaling
Variable Importance in Projection (VIP)	vip vip,m8_model-method
Extract model weights	weights weights,m8_model-method
Compute X residual matrix Returns the residual matrix (E) of an OPLS model.	xres xres,m8_model-method