aggregate_samples       Aggregate samples
airPLS_fast_dataset     Baseline correction of Raman and SERS spectra
                        using airPLS
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
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
filter_feature_selection
                        Feature Selection Using Univariate Filters
flat_pattern_filter     Flat pattern filter
get_MetabolitePath      Returns an object of KEGGPathway of the pathway
                        especified in pathcode
get_OrganismsCodes      Get code, t number, full name and phylogeny of
                        all organisms in KEGG:
get_cpd_names           Get compound names from KEGG codes
get_metabPaths_org      Get vector with paths numbers that occur in the
                        given organism, named with the full path name:
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_paths_with_cpds_org
                        Get only the paths of the organism that contain
                        given compounds:
get_x_label             Get x label
get_x_values_as_text    Get x values as text
ica_analysis_dataset    ICA analysis
ica_kmeans_plot2D       ICA 2D k-means plot
ica_kmeans_plot3D       ICA 3D k-means plot
ica_loadingsplot        ICA loadings plot
ica_pairs_kmeans_plot   ICA pairs k-means plot
ica_pairs_plot          ICA pairs plot
ica_scoresplot2D        ICA 2D scores plot
ica_scoresplot3D        ICA 3D scores plot
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 present in the pathway, it is
                        coloured differently.
pca_analysis_dataset    Classical PCA analysis
pca_biplot              PCA biplot
pca_biplot3D            PCA 3D biplot
pca_importance          PCA component importance
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_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
raman_align_peaks       Align detected peaks across spectra into
                        wavenumber bins
raman_crop_spectra      Crop Raman or SERS spectra to a wavenumber
                        interval
raman_despike           Remove spikes from Raman or SERS spectra
raman_find_peaks        Find peaks in Raman or SERS spectra
raman_normalize         Normalize Raman or SERS spectra
raman_normalize_peak_features
                        Normalize peak feature matrix
raman_sgolay_derivative
                        Compute Savitzky-Golay second derivative of
                        Raman or SERS spectra
raman_transform_fourier
                        Extract Fourier power features from Raman or
                        SERS spectra
raman_transform_wavelet
                        Extract Haar wavelet features from Raman or
                        SERS spectra
read_csvs_folder        Read all CSV peak files in a folder
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_multiple_csvs      Read multiple CSV peak files
read_spc_nosubhdr       Import for Thermo Galactic's spc file format
                        These functions allow to import .spc files. A
                        detailed description of the .spc file format is
                        available at
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
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
tsne_analysis_dataset   t-SNE analysis
tsne_kmeans_plot2D      t-SNE 2D k-means plot
tsne_kmeans_plot3D      t-SNE 3D k-means plot
tsne_pairs_kmeans_plot
                        t-SNE pairs k-means plot
tsne_pairs_plot         t-SNE pairs plot
tsne_scoresplot2D       t-SNE 2D scores plot
tsne_scoresplot3D       t-SNE 3D scores plot
umap_analysis_dataset   UMAP analysis
umap_kmeans_plot2D      UMAP 2D k-means plot
umap_kmeans_plot3D      UMAP 3D k-means plot
umap_pairs_kmeans_plot
                        UMAP pairs k-means plot
umap_pairs_plot         UMAP pairs plot
umap_scoresplot2D       UMAP 2D scores plot
umap_scoresplot3D       UMAP 3D scores plot
