Automated spectraL Processing System for NMR

Documentation for package ‘AlpsNMR’ version 4.2.0

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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