API for specmine
Metabolomics and Spectral Data Analysis and Mining
| Global functions | |
|---|---|
| .spc.ylab | Source code |
| Hyper_method | Source code |
| Hyper_uniq_method | Source code |
| MAIT_identify_metabolites | Man page Source code |
| Match_uniq_method | Source code |
| absorbance_to_transmittance | Man page Source code |
| aggregate_samples | Man page |
| aov_all_vars | Man page |
| apply_by_group | Man page |
| apply_by_groups | Man page |
| apply_by_sample | Man page |
| apply_by_variable | Man page |
| background_correction | Man page Source code |
| baseline_correction | Man page Source code |
| boxplot_variables | Man page |
| boxplot_vars_factor | Man page Source code |
| calculate_ellipses | Source code |
| check_2d_dataset | Man page |
| check_dataset | Man page |
| clustering | Man page Source code |
| compare_regions_by_sample | Man page |
| compounds_in_group | Source code |
| compounds_in_organism | Source code |
| convert_chebi_to_kegg | Man page Source code |
| convert_chebi_to_spcmnm | Source code |
| convert_from_chemospec | Man page Source code |
| convert_hmdb_to_kegg | Man page Source code |
| convert_keggpathway_2_reactiongraph | Man page Source code |
| convert_multiple_spcmnm_to_kegg | Man page Source code |
| convert_spcmnm_to_kegg | Source code |
| convert_to_factor | Man page |
| correlation_test | Man page Source code |
| correlations_dataset | Man page Source code |
| correlations_test | Man page Source code |
| count_missing_values | Man page |
| count_missing_values_per_sample | Man page |
| count_missing_values_per_variable | Man page |
| create_2d_dataset | Man page |
| create_dataset | Man page |
| create_metaboanalyst_mat | Source code |
| create_pathway_with_reactions | Man page Source code |
| cubic_root_transform | Man page |
| cv | Source code |
| data_correction | Man page |
| dataset_from_peaks | Man page |
| dendrogram_plot | Man page |
| dendrogram_plot_col | Man page |
| descendMin | Source code |
| detect_nmr_peaks | Source code |
| detect_nmr_peaks_from_dataset | Man page Source code |
| feature_selection | Man page Source code |
| filter_feature_selection | Man page Source code |
| findEqualGreaterM | Source code |
| find_equal_samples | Man page |
| first_derivative | Man page Source code |
| flat_pattern_filter | Man page |
| fold_change | Man page Source code |
| fold_change_var | Man page Source code |
| get_MetabolitePath | Man page Source code |
| get_OrganismsCodes | Man page Source code |
| get_cpd_names | Man page Source code |
| get_data | Man page |
| get_data_as_df | Man page |
| get_data_value | Man page |
| get_data_values | Man page |
| get_files_list_per_assay | Man page Source code |
| get_kegg_groups | Source code |
| get_metabPaths_org | Man page Source code |
| get_metabolights_study | Man page Source code |
| get_metabolights_study_files_assay | Man page Source code |
| get_metabolights_study_metadata_assay | Man page Source code |
| get_metabolights_study_samples_files | Man page Source code |
| get_metadata | Man page |
| get_metadata_value | Man page |
| get_metadata_var | Man page |
| get_organisms_in_group | Source code |
| get_paths_with_cpds_org | Man page Source code |
| get_peak_values | Man page |
| get_sample_2d_data | Man page |
| get_sample_names | Man page |
| get_samples_names_dx | Man page |
| get_samples_names_spc | Man page Source code |
| get_spcmnm_from_spcmns | Source code |
| get_type | Man page |
| get_value_label | Man page |
| get_x_label | Man page |
| get_x_values_as_num | Man page |
| get_x_values_as_text | Man page |
| group_peaks | Man page |
| group_peaks_metaboanalyst | Source code |
| heatmap_correlations | Man page Source code |
| hierarchical_clustering | Man page Source code |
| identification_nmr_peaks | Source code |
| impute_nas_knn | Man page |
| impute_nas_linapprox | Man page Source code |
| impute_nas_mean | Man page |
| impute_nas_median | Man page |
| impute_nas_value | Man page |
| indexes_to_xvalue_interval | Man page |
| isPositive | Source code |
| is_compound_in_entity | Source code |
| is_compound_in_group | Source code |
| is_compound_in_organism | Source code |
| is_group | Source code |
| is_organism | Source code |
| is_spectra | Man page |
| is_windows | Source code |
| kmeans_clustering | Man page Source code |
| kmeans_plot | Man page Source code |
| kmeans_result_df | Man page Source code |
| kruskalTest_dataset | Man page Source code |
| ksTest_dataset | Man page Source code |
| linreg_all_vars | Man page |
| linreg_coef_table | Man page Source code |
| linreg_pvalue_table | Man page Source code |
| linreg_rsquared | Man page Source code |
| linregression_onevar | Man page |
| localMax | Source code |
| log_transform | Man page |
| low_level_fusion | Man page |
| match_Hyper | Source code |
| match_Match_uniq | Source code |
| mean_centering | Man page Source code |
| merge_data_metadata | Man page |
| merge_datasets | Man page |
| metabolights_studies_list | Man page Source code |
| metadata_as_variables | Man page Source code |
| missingvalues_imputation | Man page |
| ms_create_matrix | Source code |
| ms_fill_peaks | Source code |
| ms_rt_correction | Source code |
| msc_correction | Man page |
| multiClassSummary | Man page |
| multifactor_aov_all_vars | Man page |
| multifactor_aov_pvalues_table | Man page Source code |
| multifactor_aov_varexp_table | Man page Source code |
| multiplot | Man page Source code |
| nmr_identification | Man page Source code |
| normalize | Man page |
| normalize_samples | Man page |
| num_samples | Man page |
| num_x_values | Man page |
| offset_correction | Man page Source code |
| pathway_analysis | Man page Source code |
| pca_analysis_dataset | Man page Source code |
| pca_biplot | Man page Source code |
| pca_biplot3D | Man page Source code |
| pca_importance | Man page Source code |
| pca_kmeans_plot2D | Man page Source code |
| pca_kmeans_plot3D | Man page Source code |
| pca_pairs_kmeans_plot | Man page Source code |
| pca_pairs_plot | Man page Source code |
| pca_plot_3d | Man page |
| pca_robust | Man page Source code |
| pca_scoresplot2D | Man page Source code |
| pca_scoresplot3D | Man page Source code |
| pca_scoresplot3D_rgl | Man page Source code |
| pca_screeplot | Man page Source code |
| peak_detection2d | Man page Source code |
| peaklist | Source code |
| peaks_per_sample | Man page |
| peaks_per_samples | Man page |
| peaks_to_dataset | Source code |
| plot_2d_spectra | Man page Source code |
| plot_anova | Man page Source code |
| plot_fold_change | Man page Source code |
| plot_kruskaltest | Man page Source code |
| plot_kstest | Man page Source code |
| plot_peaks | Man page Source code |
| plot_regression_coefs_pvalues | Man page Source code |
| plot_spectra | Man page |
| plot_spectra_simple | Man page |
| plot_ttests | Man page Source code |
| plotvar_twofactor | Man page Source code |
| predict_samples | Man page Source code |
| readBruker | Source code |
| read_Bruker_files | Man page Source code |
| read_Bruker_files_2d | Man page Source code |
| read_csvs_folder | Man page |
| read_data_csv | Man page |
| read_data_dx | Man page |
| read_data_spc | Man page |
| read_dataset_csv | Man page |
| read_dataset_dx | Man page |
| read_dataset_spc | Man page |
| read_metadata | Man page |
| read_ms_spec | Source code |
| read_ms_spectra | Man page Source code |
| read_multiple_csvs | Man page |
| read_spc_nosubhdr | Man page |
| read_varian_2dspectra_raw | Man page Source code |
| read_varian_2dspectrum_raw | Source code |
| read_varian_spectra_raw | Man page Source code |
| read_varian_spectrum_raw | Source code |
| rectUnique | Source code |
| recursive_feature_elimination | Man page Source code |
| remove_data | Man page |
| remove_data_variables | Man page |
| remove_metadata_variables | Man page |
| remove_peaks_interval | Man page |
| remove_peaks_interval_sample_list | Man page |
| remove_samples | Man page |
| remove_samples_by_na_metadata | Man page |
| remove_samples_by_nas | Man page |
| remove_variables_by_nas | Man page |
| remove_x_values_by_interval | Man page |
| replace_data_value | Man page |
| replace_metadata_value | Man page |
| savitzky_golay | Man page Source code |
| scale_to_interval | Source code |
| scaling | Man page |
| scaling_samples | Man page |
| score_freq | Source code |
| score_organism | Source code |
| score_solvent | Source code |
| set_groups_metaboanalyst | Source code |
| set_metadata | Man page |
| set_sample_names | Man page |
| set_value_label | Man page |
| set_x_label | Man page |
| set_x_values | Man page |
| shift_correction | Man page |
| smoothing_interpolation | Man page Source code |
| smoothing_spcbin | Source code |
| smoothing_spcloess | Source code |
| snr_all | Source code |
| snr_spectra | Source code |
| snv_dataset | Man page Source code |
| specmine.bin | Source code |
| specmine.loess | Source code |
| spectra_options | Man page |
| stats_by_sample | Man page |
| stats_by_variable | Man page |
| subset_by_samples_and_xvalues | Man page |
| subset_metadata | Man page |
| subset_random_samples | Man page |
| subset_samples | Man page |
| subset_samples_by_metadata_values | Man page |
| subset_x_values | Man page |
| subset_x_values_by_interval | Man page |
| sum_2d_dataset | Man page |
| sum_dataset | Man page |
| summary_var_importance | Man page Source code |
| tTests_dataset | Man page Source code |
| tTests_pvalue | Source code |
| trainClassifier | Source code |
| train_and_predict | Man page Source code |
| train_classifier | Man page Source code |
| train_models_performance | Man page Source code |
| transform_data | Man page |
| transmittance_to_absorbance | Man page Source code |
| trim | Source code |
| uniqueness_scores | Source code |
| values_per_peak | Man page |
| values_per_sample | Man page |
| var_importance | Source code |
| variables_as_metadata | Man page Source code |
| volcano_plot_fc_tt | Man page Source code |
| wavelength.seq | Source code |
| wavelengths | Source code |
| x_values_to_indexes | Man page |
| xvalue_interval_to_indexes | Man page |
