Man pages for specmine
Metabolomics and Spectral Data Analysis and Mining
| aggregate_samples | Aggregate samples |
| aov_all_vars | Analysis of variance |
| aov_one_var | Analysis of variance for one variable |
| apply_by_group | Apply by group |
| apply_by_groups | Apply by groups |
| baseline_correction | Auto-exported function: baseline_correction |
| convert_chebi_to_kegg | Get kegg codes from chebi codes: |
| convert_from_chemospec | Auto-exported function: convert_from_chemospec |
| convert_hmdb_to_kegg | Get kegg codes from hmdb codes: |
| convert_keggpathway_2_reactiongraph | Convert KEGGPathway object to graph object |
| convert_multiple_spcmnm_to_kegg | Get kegg codes from spcmnm codes: |
| 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_dataset | Create dataset |
| create_pathway_with_reactions | Creates the pathway, with reactions included in the nodes |
| dataset_from_peaks | Create a dataset from peak lists |
| feature_selection | Auto-exported function: feature_selection |
| filter_feature_selection | Feature Selection Using Univariate Filters |
| flat_pattern_filter | Flat pattern filter |
| get_cpd_names | Get compound names from KEGG codes |
| get_files_list_per_assay | Auto-exported function: get_files_list_per_assay |
| get_metabolights_study | Download a complete MetaboLights study |
| get_metabolights_study_files_assay | Download files for one MetaboLights assay |
| get_metabolights_study_metadata_assay | Get metadata for one MetaboLights assay |
| get_metabolights_study_samples_files | Get sample-file mapping for one MetaboLights assay |
| get_MetabolitePath | Returns an object of KEGGPathway of the pathway especified in... |
| get_metabPaths_org | Get vector with paths numbers that occur in the given... |
| get_OrganismsCodes | Get code, t number, full name and phylogeny of all organisms... |
| get_paths_with_cpds_org | Get only the paths of the organism that contain given... |
| get_peak_values | Auto-exported function: get_peak_values |
| get_samples_names_dx | Auto-exported function: get_samples_names_dx |
| get_x_label | Get x label |
| get_x_values_as_text | Get x values as text |
| impute_nas_knn | Impute missing values with kNN |
| impute_nas_mean | Impute missing values with mean |
| impute_nas_median | Impute missing values with median |
| impute_nas_value | Impute missing values with a constant |
| merge_data_metadata | Merge data and metadata |
| metabolights_studies_list | List public MetaboLights studies |
| missingvalues_imputation | Missing values imputation |
| multiClassSummary | Multi-class summary metrics |
| pathway_analysis | Creates the pathway wanted. If any of the given compounds is... |
| pca_analysis_dataset | Auto-exported function: pca_analysis_dataset |
| pca_biplot | PCA biplot |
| pca_biplot3D | PCA 3D biplot |
| pca_kmeans_plot2D | PCA 2D k-means plot |
| pca_kmeans_plot3D | PCA 3D k-means plot |
| pca_pairs_kmeans_plot | PCA pairs plot with k-means clusters |
| pca_pairs_plot | PCA pairs plot |
| pca_plot_3d | Auto-exported function: pca_plot_3d |
| pca_robust | Robust PCA analysis |
| pca_scoresplot2D | PCA 2D scores plot |
| pca_scoresplot3D | PCA 3D scores plot |
| pca_scoresplot3D_rgl | PCA 3D scores plot using rgl |
| pca_screeplot | PCA scree plot |
| peak_detection2d | Detect peaks in 2D NMR spectra |
| read_csvs_folder | Read all CSV peak files in a folder |
| read_data_csv | Reads a data matrix from a CSV file |
| read_data_dx | Read JDX spectra files from a folder |
| read_dataset_csv | Reads a dataset from CSV files |
| read_dataset_dx | Read a dataset from JDX files |
| read_metadata | Reads metadata from a CSV file |
| read_ms_spectra | Auto-exported function: read_ms_spectra |
| read_multiple_csvs | Read multiple CSV peak files |
| read-spc | Import for Thermo Galactic's spc file format These functions... |
| recursive_feature_elimination | Recursive Feature Elimination |
| remove_data | Remove data |
| remove_data_variables | Remove data variables |
| remove_metadata_variables | Remove metadata variables |
| remove_samples | Remove samples |
| remove_samples_by_na_metadata | Remove samples by NA 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 |
| specmine-package | specmine: Metabolomics data analysis tools |
| spectra_options | Spectra processing options |
| 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 |
| summary_var_importance | Summarise variable importance tables |
| train_and_predict | Train a classifier and predict new samples |
| train_classifier | Train a classifier |
| train_models_performance | Train multiple models and compare their performance |
