Package index

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

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

to_ASICS(): Export data for the ASICS spectral quantification library

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

nmr_autophase(): Rephase 1D NMR data