Man pages for sipss/AlpsLCMS
Signal processing of LC-MS metabolomics
| adjustRT | Peak alignment |
| assignation_neg_HMDB | HMDB metabolites in negative ionization |
| assignation_pos_HMDB | HMDB metabolites in positive ionization |
| bp_kfold_VIP_analysis | K-fold bootstrap and permutation over PLS-VIP |
| bp_VIP_analysis | Bootstrap and permutation over PLS-VIP |
| check_dataset | check_dataset |
| clustering | Clustering |
| cromplot | cromplot |
| default_peakpicking_params | Default parameters for peak picking optimization |
| do_findmain | Cluster annotation |
| feature_reduction | Feature reduction |
| feature_values | Feature table |
| filterMassAcquisition | Filter a mass window |
| find_peaks_cwp | Chromatographic peak detection (CentWave) |
| getRamSt | Get st parameter value for clustering |
| groupPeaks | Peak correspondence |
| HMDB_db | The Human Metabolome DataBase template: Table with... |
| install_RawConverter | Download and Install RawConverter |
| IPO_group_peaks | Peak Correspondence |
| is.negative | is.negative |
| is.positive | is.positive |
| known_metabolites | Known metabolites in the dataset |
| lcms_convert_ipo_to_xcms | Converts IPO parameters to XCMS format |
| lcms_data_analysis | Data analysis |
| lcms_data_analysis_method | Create method for lcms data analysis |
| lcms_dataset_load | Load lcms_datasets |
| lcms_dataset_save | Save lcms_datasets |
| lcms_default_retcorgroup_params | Default parameters for optimization of retention time... |
| lcms_diagnose | Set/Get diagnostic information |
| lcms_fill_chrom_peaks | Filling missing values in a peak table |
| lcms_filter_mz | Filter by mass/charge |
| lcms_filter_polarity | Filter an experiment by its polarity |
| lcms_filter_rt_min | Filter by retention time |
| lcms_filter_sample_type | Filter by sample type |
| lcms_identify_metabolites | Metabolite search |
| lcms_list_mzxml_samples | RAW converter |
| lcms_meta_add | Add metadata |
| lcms_meta_export | Export metadata |
| lcms_meta_read | Read metadata |
| lcms_peak_annotation | Peak Annotation |
| lcms_peak_table_boxplots | Boxplots for the significant peak table features |
| lcms_peak_table_pca | Principal Component Analysis (PCA) |
| lcms_plot_chrom | Base peak chromatogram |
| lcms_plot_chrom_peak_image | Image of Chromatographic Peaks by sample |
| lcms_plot_metabolites | Metabolite Candidates |
| lcms_plot_tics | Total Ion Count (TIC) plot |
| lcms_raw_data | Raw data extractor from a MAIT object |
| lcms_raw_to_mzxml | Raw to mzxml |
| lcms_read_ipo_to_xcms | Read IPO parameters to XCMS format |
| lcms_read_samples | Read mzXML samples |
| lcms_rearrange_datafiles_by_class | Rearrange datafiles by class |
| lcms_retcorgroup_optimization | Optimization of retention time correction and grouping... |
| lcms_retention_time_alignment_plot | Retention Time Correction Plot |
| lcms_sig_peaks_table | Significant feature information |
| lcms_spectral_sig_features | Extract significant features from a MAIT object |
| lcms_tics | Total Ion Count (TIC) |
| lcms_to_mait | Convert xcms to MAIT |
| lcms_write_opt_params | Displaying and Storing optimized settings |
| lcms_write_parameter_table | Write parameter table |
| models_stability_plot_bootstrap | Models stability plot |
| models_stability_plot_plsda | Models stability plot |
| obiAdjust_Rtime | Retention Time Correction |
| PeakDensityPar | Peak density parameters |
| PeakGroupsPar | Peak density parameters |
| peakpicking_optimization | Peak picking optimization |
| permutation_test_model | Permutation test |
| permutation_test_plot | Permutation test plot |
| phData | Generic function to access the phenotypic data (Biobase) |
| 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 lcms_data_analysis (PLSDA model with AUROC and VIP... |
| random_subsampling | Random subsampling |
| reexports | Objects exported from other packages |
