Man pages for specmine
Metabolomics and Spectral Data Analysis and Mining
| absorbance_to_transmittance | Convert absorbance to transmittance |
| aggregate_samples | Aggregate samples |
| aov_all_vars | Analysis of variance |
| apply_by_group | Apply by group |
| apply_by_groups | Apply by groups |
| apply_by_sample | Apply function to samples |
| apply_by_variable | Apply function to variables |
| background_correction | Background correction |
| baseline_correction | Baseline correction |
| boxplot_variables | Boxplot of variables |
| boxplot_vars_factor | Boxplot of variables with metadata's variable factors |
| check_2d_dataset | Check 2D dataset. |
| check_dataset | Check dataset |
| clustering | Perform cluster analysis |
| compare_regions_by_sample | Compare regions by sample |
| convert_chebi_to_kegg | Convert CHEBI codes to KEGG codes. |
| convert_from_chemospec | Convert from ChemoSpec |
| convert_hmdb_to_kegg | Convert HMDB codes to KEGG codes. |
| convert_keggpathway_2_reactiongraph | Convert KEGGPathway object to graph object. |
| convert_multiple_spcmnm_to_kegg | Convert specmine metabolite codes to KEGG codes. |
| convert_to_factor | Convert metadata to factor |
| correlations_dataset | Dataset correlations |
| correlations_test | Correlations test |
| correlation_test | Correlation test of two variables or samples |
| count_missing_values | Count missing values |
| count_missing_values_per_sample | Count missing values per sample |
| count_missing_values_per_variable | Count missing values per variable |
| create_2d_dataset | Create 2D dataset |
| create_dataset | Create dataset |
| create_pathway_with_reactions | Creates the pathway, with reactions included in the nodes. |
| cubic_root_transform | Cubic root transformation |
| data_correction | Data correction |
| dataset_from_peaks | Dataset from peaks |
| dendrogram_plot | Plot dendrogram |
| dendrogram_plot_col | Plot dendrogram |
| detect_nmr_peaks_from_dataset | Detection of the peaks in an NMR spectra dataset. |
| feature_selection | Perform feature selection |
| filter_feature_selection | Perform selection by filter |
| find_equal_samples | Find equal samples |
| first_derivative | First derivative |
| flat_pattern_filter | Flat pattern filter |
| fold_change | Fold change analysis |
| fold_change_var | Fold change applied on two variables |
| get_cpd_names | Get the names of the compounds that correspond to the kegg... |
| get_data | Get data |
| get_data_as_df | Get data as data frame |
| get_data_value | Get data value |
| get_data_values | Get data values |
| get_files_list_assay | Get list of files per assay for MetaboLights study. |
| get_metabolights_study | Download MetaboLights study files. |
| get_metabolights_study_files_assay | Download data files from an assay of MetaboLights study |
| get_metabolights_study_metadata_assay | Download metadata file from an assay of MetaboLights study |
| get_metabolights_study_samples_files | Get list of files from an assay of the MetaboLights study and... |
| get_MetabolitePath | Returns an object of KEGGPathway of the pathway especified in... |
| get_metabPaths_org | Get the metabolic pathways present in given organism. |
| get_metadata | Get metadata |
| get_metadata_value | Get metadata value |
| get_metadata_var | Get metadata variable |
| get_OrganismsCodes | Get all organisms in KEGG. |
| get_paths_with_cpds_org | Get only the paths of the organism that contain one or more... |
| get_peak_values | Get peak values |
| get_sample_2d_data | Get data |
| get_sample_names | Get sample names |
| get_samples_names_dx | Get sample's names from DX files |
| get_samples_names_spc | Get sample's names from SPC files |
| get_type | Get type of data |
| get_value_label | Get value label |
| get_x_label | Get x-axis label |
| get_x_values_as_num | Get x-axis values as numbers |
| get_x_values_as_text | Get x-axis values as text |
| group_peaks | Group peaks |
| heatmap_correlations | Correlations heatmap |
| hierarchical_clustering | Perform hierarchical clustering analysis |
| impute_nas_knn | Impute missing values with KNN |
| impute_nas_linapprox | Impute missing values with linear approximation |
| impute_nas_mean | Impute missing values with mean |
| impute_nas_median | Impute missing values with median |
| impute_nas_value | Impute missing values with value replacement |
| indexes_to_xvalue_interval | Get the x-values of a vector of indexes |
| is_spectra | Check type of data |
| kmeans_clustering | Perform k-means clustering analysis |
| kmeans_plot | Plot kmeans clusters |
| kmeans_result_df | Show cluster's members |
| kruskalTest_dataset | Kruskal-Wallis tests on dataset |
| ksTest_dataset | Kolmogorov-Smirnov tests on dataset |
| linreg_all_vars | Linear Regression |
| linreg_coef_table | Linear regression coefficient table |
| linreg_pvalue_table | Linear regression p-values table |
| linregression_onevar | Linear regression on one variable |
| linreg_rsquared | Linear regression r-squared |
| log_transform | Logarithmic transformation. |
| low_level_fusion | Low level fusion |
| MAIT_identify_metabolites | MAIT metabolite identification |
| mean_centering | Mean centering |
| merge_data_metadata | Merge data and metadata |
| merge_datasets | Merge two datasets |
| metabolights_studies_list | List the study IDs available in the MetaboLights database. |
| metadata_as_variables | Metadata as variables |
| missingvalues_imputation | Missing values imputation |
| msc_correction | Multiplicative scatter correction |
| multiClassSummary | Multi Class Summary |
| multifactor_aov_all_vars | Multifactor ANOVA |
| multifactor_aov_pvalues_table | Multifactor ANOVA p-values table |
| multifactor_aov_varexp_table | Multifactor ANOVA variability explained table |
| multiplot | Multiplot |
| nmr_identification | NMR metabolite identification |
| normalize | Normalize data |
| normalize_samples | Normalize samples |
| num_samples | Get number of samples |
| num_x_values | Get number of x values |
| offset_correction | Offset correction |
| pathway_analysis | Creates the metabolic pathway wanted. If any of the given... |
| pca_analysis_dataset | PCA analysis (classical) |
| pca_biplot | PCA biplot |
| pca_biplot3D | 3D PCA biplot (interactive) |
| pca_importance | PCA importance |
| pca_kmeans_plot2D | 2D PCA k-means plot |
| pca_kmeans_plot3D | 3D PCA k-means plot (interactive) |
| pca_pairs_kmeans_plot | PCA k-means pairs plot |
| pca_pairs_plot | PCA pairs plot |
| pca_plot_3d | 3D pca plot |
| pca_robust | PCA analysis (robust) |
| pca_scoresplot2D | 2D PCA scores plot |
| pca_scoresplot3D | 3D PCA scores plot |
| pca_scoresplot3D_rgl | 3D PCA scores plot (interactive) |
| pca_screeplot | PCA scree plot |
| peak_detection2d | Detection of the peaks in an 2D NMR spectra dataset. |
| peaks_per_sample | Peaks per sample |
| peaks_per_samples | Peaks per samples |
| plot_2d_spectra | Plot of 2D spectra |
| plot_anova | Plot ANOVA results |
| plot_fold_change | Plot fold change results |
| plot_kruskaltest | Plot Kruskal-Wallis tests results |
| plot_kstest | Plot Kolmogorov-Smirnov tests results |
| plot_peaks | Plot the peaks of a MS or NMR dataset. |
| plot_regression_coefs_pvalues | Plot regression coefficient and p-values |
| plot_spectra | Plot spectra |
| plot_spectra_simple | Plot spectra (simple) |
| plot_ttests | Plot t-tests results |
| plotvar_twofactor | Plot variable distribution on two factors |
| predict_samples | Predict samples |
| read_Bruker_files | Read Bruker processed spectra. |
| read_Bruker_files_2d | Read Bruker processed 2D spectra. |
| read_csvs_folder | Read CSVs from folder |
| read_data_csv | Read CSV data |
| read_data_dx | Read data from (J)DX files |
| read_dataset_csv | Read dataset from CSV |
| read_dataset_dx | Read dataset from (J)DX files |
| read_dataset_spc | Read dataset from SPC files |
| read_data_spc | Read data from SPC files |
| read_metadata | Read metadata |
| read_ms_spectra | Read MS spectra |
| read_multiple_csvs | Read multiple CSVs |
| read-spc | Import for Thermo Galactic's spc file format These functions... |
| read_varian_2dspectra_raw | Function that reads raw 2D spectra (intensity over time... |
| read_varian_spectra_raw | Function that reads raw spectra (intensity over time spectra)... |
| recursive_feature_elimination | Perform recursive feature elimination |
| remove_data | Remove data |
| remove_data_variables | Remove data variables |
| remove_metadata_variables | Remove metadata's variables |
| remove_peaks_interval | Remove interval of peaks |
| remove_peaks_interval_sample_list | Remove interval of peaks (sample list) |
| remove_samples | Remove samples |
| remove_samples_by_na_metadata | Remove samples by NA on metadata |
| remove_samples_by_nas | Remove samples by NAs |
| remove_variables_by_nas | Remove variables by NAs |
| remove_x_values_by_interval | Remove x-values by interval |
| replace_data_value | Replace data value |
| replace_metadata_value | Replace metadata's value |
| savitzky_golay | Savitzky-golay transformation |
| scaling | Scale dataset |
| scaling_samples | Scale data matrix |
| set_metadata | Set new metadata |
| set_sample_names | Set samples names |
| set_value_label | Set value label |
| set_x_label | Set x-label |
| set_x_values | Set new x-values |
| shift_correction | Shift correction |
| smoothing_interpolation | Smoothing interpolation |
| snv_dataset | Standard Normal Variate |
| spectra_options | Information on the library of NMR reference spectra in our... |
| stats_by_sample | Statistics of samples |
| stats_by_variable | Statistics of variables |
| subset_by_samples_and_xvalues | Subset by samples and x-values |
| subset_metadata | Subset metadata |
| subset_random_samples | Subset random samples |
| subset_samples | Subset samples |
| subset_samples_by_metadata_values | Subset samples by metadata values |
| subset_x_values | Subset x-values |
| subset_x_values_by_interval | Subset x-values by interval |
| sum_2d_dataset | 2D Dataset summary |
| sum_dataset | Dataset summary |
| summary_var_importance | Summary of variables importance |
| train_and_predict | Train and predict |
| train_classifier | Train classifier |
| train_models_performance | Train models |
| transform_data | Transform data |
| transmittance_to_absorbance | Convert transmittance to absorbance |
| tTests_dataset | t-Tests on dataset |
| values_per_peak | Values per peak |
| values_per_sample | Values per peak |
| variables_as_metadata | Variables as metadata |
| volcano_plot_fc_tt | Volcano plot |
| xvalue_interval_to_indexes | Get indexes of an interval of x-values |
| x_values_to_indexes | Get x-values indexes |
