Automated spectraL Processing System for NMR
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Documentation for package ‘AlpsNMR’ version 4.11.0
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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_autophase | Rephase 1D NMR data |
| 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_ASICS | Export data for the ASICS spectral quantification library |
| 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 |