# Automated spectraL Processing System for NMR

## Documentation for package ‘AlpsNMR’ version 4.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B D F G H I L M N P R S T V misc

AlpsNMR-package | AlpsNMR: Automated spectraL Processing System for NMR

## -- A --

AlpsNMR | AlpsNMR: Automated spectraL Processing System for NMR
as.data.frame.nmr_dataset_peak_table | nmr_dataset_peak_table (S3 class)

## -- B --

bp_kfold_VIP_analysis | K-fold bootstrap and permutation over PLS-VIP
bp_VIP_analysis | Bootstrap and permutation over PLS-VIP

## -- D --

download_MTBLS242 | Download MTBLS242

## -- F --

files_to_rDolphin | Files to rDoplhin
file_lister | NMR file lister
filter.nmr_dataset_family | Keep samples based on metadata column criteria
format.nmr_dataset | Format for nmr_dataset
format.nmr_dataset_1D | format for nmr_dataset_1D
format.nmr_dataset_peak_table | Format for nmr_dataset_peak_table

## -- G --

get_integration_with_metadata | Get integrals with metadata from integrate peak positions

## -- H --

hmdb | The Human Metabolome DataBase multiplet table
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

## -- I --

is.nmr_dataset | Object is of nmr_dataset class
is.nmr_dataset_1D | Object is of nmr_dataset_1D class
is.nmr_dataset_peak_table | Object is of nmr_dataset_peak_table class

## -- L --

load_and_save_functions | nmr_dataset_load

## -- M --

models_stability_plot_bootstrap | Models stability plot
models_stability_plot_plsda | Models stability plot

## -- N --

new_nmr_dataset | Create an nmr_dataset object
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_data_analysis_method | Create method for NMR data analysis
nmr_align | Align NMR spectra
nmr_align_find_ref | Find alignment reference
nmr_baseline_estimation | Estimate the baseline on an nmr_dataset_1D object, using baseline::baseline.als.
nmr_baseline_removal | Baseline Removal NMR
nmr_baseline_threshold | Threshold estimation for peak detection
nmr_baseline_threshold_plot | Plot the baseline thresholds
nmr_batman | Batman helpers
nmr_batman_export_dataset | Batman helpers
nmr_batman_metabolites_list | Batman helpers
nmr_batman_multi_data_user | Batman helpers
nmr_batman_multi_data_user_hmdb | Batman helpers
nmr_batman_options | Batman Options helper
nmr_batman_write_options | Batman helpers
nmr_build_peak_table | Build a peak table from the clustered peak list
nmr_data | Set/Return the full spectra matrix
nmr_data.nmr_dataset_1D | Set/Return the full spectra matrix
nmr_data<- | Set/Return the full spectra matrix
nmr_data<-.nmr_dataset_1D | Set/Return the full spectra matrix
nmr_dataset | nmr_dataset (S3 class)
nmr_dataset_1D | nmr_dataset_1D (S3 class)
nmr_dataset_family | nmr_dataset like objects (S3 classes)
nmr_dataset_load | nmr_dataset_load
nmr_dataset_peak_table | nmr_dataset_peak_table (S3 class)
nmr_dataset_peak_table_to_SummarizedExperiment | Export nmr_dataset_peak_table to SummarizedExperiment
nmr_dataset_save | nmr_dataset_load
nmr_data_1r_to_SummarizedExperiment | Export 1D NMR data to SummarizedExperiment
nmr_data_analysis | Data analysis
nmr_data_analysis_method | Create method for NMR data analysis
nmr_detect_peaks | Peak detection for NMR
nmr_detect_peaks_plot | Plot peak detection results
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_tune_snr | Diagnose SNR threshold in peak detection
nmr_exclude_region | Exclude region from samples
nmr_exclude_region.nmr_dataset_1D | Exclude region from samples
nmr_export_data_1r | Export 1D NMR data to a CSV file
nmr_get_peak_distances | Compute peak to peak distances
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)
nmr_integrate_peak_positions | Integrate peak positions
nmr_integrate_regions | Integrate regions
nmr_integrate_regions.nmr_dataset_1D | Integrate regions
nmr_interpolate_1D | Interpolate a set of 1D NMR Spectra
nmr_interpolate_1D.nmr_dataset | Interpolate a set of 1D NMR Spectra
nmr_meta_add | Add metadata to an nmr_dataset object
nmr_meta_add_tidy_excel | Add metadata to an nmr_dataset object
nmr_meta_export | Export Metadata to an Excel file
nmr_meta_get | Get metadata
nmr_meta_get_column | Get a single metadata column
nmr_meta_groups | Get the names of metadata groups
nmr_normalize | Normalize nmr_dataset_1D samples
nmr_normalize_extra_info | Normalize nmr_dataset_1D samples
nmr_pca_build_model | Build a PCA on for an nmr_dataset
nmr_pca_build_model.nmr_dataset_1D | Build a PCA on for an nmr_dataset
nmr_pca_loadingplot | Plotting functions for PCA
nmr_pca_outliers | Compute PCA residuals and score distance for each sample
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_plots | Plotting functions for PCA
nmr_pca_plot_variance | Plotting functions for PCA
nmr_pca_scoreplot | Plotting functions for PCA
nmr_peak_clustering | Peak clustering
nmr_peak_clustering_plot | Plot clustering results
nmr_ppm_resolution | PPM resolution of the spectra
nmr_ppm_resolution.nmr_dataset | PPM resolution of the spectra
nmr_ppm_resolution.nmr_dataset_1D | PPM resolution of the spectra
nmr_read_bruker_fid | Read Free Induction Decay file
nmr_read_samples | Read NMR samples
nmr_read_samples_dir | Read NMR samples
nmr_zip_bruker_samples | Create one zip file for each brucker sample path

## -- P --

Parameters_blood | to rDolphin
Parameters_cell | Parameters for cell samples profiling
Parameters_urine | Parameters for urine samples profiling
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_detection | Peak detection for NMR
permutation_test_model | Permutation test
permutation_test_plot | Permutation test plot
Pipelines | Pipelines
pipe_add_metadata | Pipelines
pipe_exclude_regions | Pipelines
pipe_filter_samples | Pipelines
pipe_interpolate_1D | Pipelines
pipe_load_samples | Pipelines
Pipe_normalization | Pipelines
pipe_normalization | Pipelines
pipe_outlier_detection | Pipelines
pipe_pakdet_align | Pipelines
pipe_peakdet_align | Pipelines
pipe_peak_integration | Pipelines
plot.nmr_dataset_1D | Plot an nmr_dataset_1D
plot_bootstrap_multimodel | Bootstrap plot predictions
plot_interactive | Plots in WebGL
plot_plsda_multimodel | Multi PLDSA model plot predictions
plot_plsda_samples | Plot PLSDA predictions
plot_vip_scores | Plot vip scores of bootstrap
plot_webgl | Plot a dataset into a HTML file
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)
ppm_resolution | Unlisted PPM resolution
print.nmr_dataset | Print for nmr_dataset
print.nmr_dataset_1D | print for nmr_dataset_1D
print.nmr_dataset_peak_table | print for nmr_dataset_peak_table

## -- R --

random_subsampling | Random subsampling
ROI_blood | ROIs for blood (plasma/serum) samples
ROI_cell | ROIs for cell samples
ROI_urine | ROIs for urine samples

## -- S --

save_files_to_rDolphin | Save files to rDoplhin
save_profiling_output | Save rDoplhin output
SummarizedExperiment_to_nmr_dataset_peak_table | Import SummarizedExperiment as mr_dataset_peak_table
SummarizedExperiment_to_nmr_data_1r | Import SummarizedExperiment as 1D NMR data

## -- T --

tidy.nmr_dataset_1D | Get a tidy data frame from nmr_data object
to_ChemoSpec | Convert to ChemoSpec Spectra class

## -- V --

validate_nmr_dataset | Validate nmr_dataset objects
validate_nmr_dataset_1D | Validate nmr_dataset objects
validate_nmr_dataset_family | Validate nmr_dataset_family objects
validate_nmr_dataset_peak_table | Validate nmr_dataset_peak_table objects

## -- misc --

[.nmr_dataset | Extract parts of an nmr_dataset
[.nmr_dataset_1D | Extract parts of an nmr_dataset_1D
[.nmr_dataset_peak_table | Extract parts of an nmr_dataset_peak_table