Function reference • AlpsNMR

Basic functions Functions you’ll use on a first analysis
`AlpsNMR` `AlpsNMR-package`	AlpsNMR: Automated spectraL Processing System for NMR
`nmr_read_samples_dir()` `nmr_read_samples()`	Read NMR samples
`nmr_meta_add()` `nmr_meta_add_tidy_excel()`	Add metadata to an nmr_dataset object
`nmr_interpolate_1D()`	Interpolate a set of 1D NMR Spectra
`nmr_exclude_region()`	Exclude region from samples
`plot(<nmr_dataset_1D>)`	Plot an nmr_dataset_1D
`nmr_baseline_removal()`	Baseline Removal NMR
`nmr_detect_peaks()`	Peak detection for NMR
`nmr_align()`	Align NMR spectra
`nmr_normalize()` `nmr_normalize_extra_info()`	Normalize nmr_dataset_1D samples
`nmr_integrate_peak_positions()`	Integrate peak positions
`nmr_data_analysis()`	Data analysis
Metadata related functions Functions to handle metadata
`nmr_meta_add()` `nmr_meta_add_tidy_excel()`	Add metadata to an nmr_dataset object
`nmr_meta_export()`	Export Metadata to an Excel file
`nmr_meta_get_column()`	Get a single metadata column
`nmr_meta_get()`	Get metadata
`nmr_meta_groups()`	Get the names of metadata groups
Import / Export functions Functions to read NMR files into AlpsNMR datasets or to export to other packages
`nmr_dataset_load()` `nmr_dataset_save()`	nmr_dataset_load
`nmr_read_bruker_fid()`	Read Free Induction Decay file
`nmr_read_samples_dir()` `nmr_read_samples()`	Read NMR samples
`nmr_zip_bruker_samples()`	Create one zip file for each brucker sample path
`nmr_export_data_1r()`	Export 1D NMR data to a CSV file
`files_to_rDolphin()`	Files to rDoplhin
`save_files_to_rDolphin()`	Save files to rDoplhin
`nmr_data_1r_to_SummarizedExperiment()`	Export 1D NMR data to SummarizedExperiment
`SummarizedExperiment_to_nmr_data_1r()`	Import SummarizedExperiment as 1D NMR data
`SummarizedExperiment_to_nmr_dataset_peak_table()`	Import SummarizedExperiment as mr_dataset_peak_table
`to_ChemoSpec()`	Convert to ChemoSpec Spectra class
`nmr_batman_options()`	Batman Options helper
`nmr_batman_write_options()` `nmr_batman_export_dataset()` `nmr_batman_multi_data_user_hmdb()` `nmr_batman_multi_data_user()` `nmr_batman_metabolites_list()`	Batman helpers
`nmr_dataset_peak_table_to_SummarizedExperiment()`	Export nmr_dataset_peak_table to SummarizedExperiment
`save_profiling_output()`	Save rDoplhin output
Data analysis / Modelling functions Functions for machine learning or data analysis, to be used once the data has been preprocessed
`bp_kfold_VIP_analysis()`	K-fold bootstrap and permutation over PLS-VIP
`bp_VIP_analysis()`	Bootstrap and permutation over PLS-VIP
`models_stability_plot_bootstrap()`	Models stability plot
`models_stability_plot_plsda()`	Models stability plot
`new_nmr_data_analysis_method()`	Create method for NMR data analysis
`nmr_data_analysis()`	Data analysis
`permutation_test_model()`	Permutation test
`permutation_test_plot()`	Permutation test plot
`plot_bootstrap_multimodel()`	Bootstrap plot predictions
`plot_plsda_multimodel()`	Multi PLDSA model plot predictions
`plot_plsda_samples()`	Plot PLSDA predictions
`plot_vip_scores()`	Plot vip scores of bootstrap
`plsda_auroc_vip_compare()`	Compare PLSDA auroc VIP results
`plsda_auroc_vip_method()`	Method for nmr_data_analysis (PLSDA model with AUROC and VIP outputs)
`random_subsampling()`	Random subsampling
nmr_dataset manipulation functions Functions to manage and filter nmr_dataset objects
`filter(<nmr_dataset_family>)`	Keep samples based on metadata column criteria
`format(<nmr_dataset_1D>)`	format for nmr_dataset_1D
`format(<nmr_dataset_peak_table>)`	Format for nmr_dataset_peak_table
`format(<nmr_dataset>)`	Format for nmr_dataset
`is.nmr_dataset_1D()`	Object is of nmr_dataset_1D class
`is.nmr_dataset_peak_table()`	Object is of nmr_dataset_peak_table class
`is.nmr_dataset()`	Object is of nmr_dataset class
`new_nmr_dataset_1D()`	Creates a new 1D nmr_dataset object from scratch
`new_nmr_dataset_peak_table()`	Creates a new nmr_dataset_peak_table object from scratch
`new_nmr_dataset()`	Create an nmr_dataset object
`nmr_data()` `nmr_data<-`()	Set/Return the full spectra matrix
`nmr_dataset_1D`	nmr_dataset_1D (S3 class)
`nmr_dataset_family`	nmr_dataset like objects (S3 classes)
`as.data.frame(<nmr_dataset_peak_table>)`	nmr_dataset_peak_table (S3 class)
`nmr_dataset`	nmr_dataset (S3 class)
`plot_interactive()`	Plots in WebGL
`plot_webgl()`	Plot a dataset into a HTML file
`plot(<nmr_dataset_1D>)`	Plot an nmr_dataset_1D
`print(<nmr_dataset_1D>)`	print for nmr_dataset_1D
`tidy(<nmr_dataset_1D>)`	Get a tidy data frame from nmr_data object
`print(<nmr_dataset_peak_table>)`	print for nmr_dataset_peak_table
`print(<nmr_dataset>)`	Print for nmr_dataset
`[`(<nmr_dataset_1D>)	Extract parts of an nmr_dataset_1D
`[`(<nmr_dataset_peak_table>)	Extract parts of an nmr_dataset_peak_table
`[`(<nmr_dataset>)	Extract parts of an nmr_dataset
`validate_nmr_dataset_family()`	Validate nmr_dataset_family objects
`validate_nmr_dataset_peak_table()`	Validate nmr_dataset_peak_table objects
`validate_nmr_dataset()` `validate_nmr_dataset_1D()`	Validate nmr_dataset objects
Metabolite identification Functions and tables related to metabolite identification
`HMDB_blood`	The Human Metabolome DataBase multiplet table: blood metabolites normally found in NMR-based metabolomics
`HMDB_cell`	The Human Metabolome DataBase multiplet table: cell metabolites normally found in NMR-based metabolomics
`HMDB_urine`	The Human Metabolome DataBase multiplet table: urine metabolites normally found in NMR-based metabolomics
`hmdb`	The Human Metabolome DataBase multiplet table
`Parameters_blood`	to rDolphin
`Parameters_cell`	Parameters for cell samples profiling
`Parameters_urine`	Parameters for urine samples profiling
`ROI_blood`	ROIs for blood (plasma/serum) samples
`ROI_cell`	ROIs for cell samples
`ROI_urine`	ROIs for urine samples
`nmr_identify_regions_blood()`	NMR peak identification (plasma/serum samples)
`nmr_identify_regions_cell()`	NMR peak identification (cell samples)
`nmr_identify_regions_urine()`	NMR peak identification (urine samples)
Alignment functions Functions to align spectra
`nmr_align_find_ref()`	Find alignment reference
`nmr_align()`	Align NMR spectra
Baseline correction Functions to remove or estimate the baseline
`nmr_baseline_removal()`	Baseline Removal NMR
`nmr_baseline_estimation()`	Estimate the baseline on an nmr_dataset_1D object, using baseline::baseline.als.
Peak detection Functions to detect peaks and visualize the resulting peak lists
`nmr_detect_peaks_plot_overview()`	Overview of the peak detection results
`nmr_detect_peaks_plot_peaks()`	Plot multiple peaks from a peak list
`nmr_detect_peaks_plot()`	Plot peak detection results
`nmr_detect_peaks_tune_snr()`	Diagnose SNR threshold in peak detection
`nmr_detect_peaks()`	Peak detection for NMR
`nmr_baseline_threshold_plot()`	Plot the baseline thresholds
`nmr_baseline_threshold()`	Threshold estimation for peak detection
`Peak_detection`	Peak detection for NMR
`peaklist_accept_peaks()`	Peak list: Create an `accepted` column based on some criteria
`peaklist_fit_lorentzians()`	Fit lorentzians to each peak to estimate areas
Peak clustering / matching / Peak tables Functions to build peak tables from peak lists
`nmr_peak_clustering()`	Peak clustering
`nmr_peak_clustering_plot()`	Plot clustering results
`nmr_build_peak_table()`	Build a peak table from the clustered peak list
`nmr_get_peak_distances()`	Compute peak to peak distances
`nmr_integrate_regions()`	Integrate regions
`nmr_integrate_peak_positions()`	Integrate peak positions
Outlier detection Functions to detect and report outliers in the dataset
`nmr_pca_build_model()`	Build a PCA on for an nmr_dataset
`nmr_pca_outliers_filter()`	Exclude outliers
`nmr_pca_outliers_plot()`	Plot for outlier detection diagnostic
`nmr_pca_outliers_robust()`	Outlier detection through robust PCA
`nmr_pca_outliers()`	Compute PCA residuals and score distance for each sample
`nmr_pca_plot_variance()` `nmr_pca_scoreplot()` `nmr_pca_loadingplot()`	Plotting functions for PCA
Other functions Other, not catalogued, AlpsNMR functions
`download_MTBLS242()`	Download MTBLS242
`file_lister()`	NMR file lister
`get_integration_with_metadata()`	Get integrals with metadata from `integrate peak positions`
`pipe_load_samples()` `pipe_add_metadata()` `pipe_interpolate_1D()` `pipe_exclude_regions()` `pipe_outlier_detection()` `pipe_filter_samples()` `pipe_peakdet_align()` `pipe_peak_integration()` `pipe_normalization()`	Pipelines
`nmr_ppm_resolution()`	PPM resolution of the spectra
`ppm_resolution()`	Unlisted PPM resolution

Reference

Basic functions

Metadata related functions

Import / Export functions

Data analysis / Modelling functions

nmr_dataset manipulation functions

Metabolite identification

Alignment functions

Baseline correction

Peak detection

Peak clustering / matching / Peak tables

Outlier detection

Other functions