Man pages for computational-metabolomics/structToolbox
Data processing & analysis tools for Metabolomics and other omics
| ANOVA | Analysis of Variance |
| as_data_frame | Convert to data.frame |
| AUC | Area under ROC curve |
| autoscale | Autoscaling |
| balanced_accuracy | Balanced Accuracy |
| blank_filter | Blank filter |
| blank_filter_hist | Histogram of blank filter fold changes |
| bootstrap | Bootstrap resampling |
| calculate | Calculate metric |
| chart_plot | chart_plot method |
| classical_lsq | Univariate Classical Least Squares Regression |
| compare_dist | Compare distributions |
| confounders_clsq | Check for confounding factors |
| confounders_lsq_barchart | Confounding factor relative change barchart |
| confounders_lsq_boxplot | Confounding factor relative change boxplot |
| constant_sum_norm | Normalisation to constant sum |
| corr_coef | Correlation coefficient |
| DatasetExperiment_boxplot | Feature distribution histogram |
| DatasetExperiment_dist | Feature distribution histogram |
| DatasetExperiment_factor_boxplot | Factor boxplot |
| DatasetExperiment_heatmap | DatasetExperiment heatmap |
| DFA | Discriminant Factor Analysis |
| dfa_scores_plot | DFA scores plot |
| dratio_filter | Dispersion ratio filter |
| equal_split | Equal group sized sampling |
| feature_boxplot | Feature boxplot |
| feature_profile | Feature profile |
| feature_profile_array | Feature profile |
| filter_by_name | Filter by name |
| filter_na_count | Minimum number of measured values filter |
| filter_smeta | Filter by sample meta data |
| fisher_exact | Fisher Exact Test |
| fold_change | Fold change |
| fold_change_int | Fold change for interactions between factors |
| fold_change_plot | Fold change plot |
| forward_selection_by_rank | Forward selection by rank |
| fs_line | Forward selection line plot |
| glog_opt_plot | Glog optimisation |
| glog_transform | Generalised logarithmic transform |
| grid_search_1d | One dimensional grid search |
| gs_line | Grid search line plot |
| HCA | Hierarchical Cluster Analysis |
| hca_dendrogram | HCA dendrogram |
| HSD | Tukey's Honest Significant Difference |
| HSDEM | Tukey's Honest Significant Difference using estimated... |
| kfoldxcv_grid | k-fold cross validation plot |
| kfoldxcv_metric | kfoldxcv metric plot |
| kfold_xval | k-fold cross-validation |
| knn_impute | kNN missing value imputation |
| kw_p_hist | Histogram of p values |
| kw_rank_sum | Kruskal-Wallis rank sum test |
| linear_model | Linear model |
| log_transform | logarithm transform |
| mean_centre | Mean centre |
| mean_of_medians | Mean of medians |
| mixed_effect | Mixed effects model |
| model_apply | Apply method |
| model_predict | Model prediction |
| model_reverse | Reverse preprocessing |
| model_train | Train a model |
| MTBLS79_DatasetExperiment | MTBLS79: Direct infusion mass spectrometry metabolomics... |
| mv_boxplot | Missing value boxplots |
| mv_feature_filter | Filter features by missing values |
| mv_feature_filter_hist | Histogram of missing values per feature |
| mv_histogram | Missing value histogram |
| mv_sample_filter | Missing value sample filter |
| mv_sample_filter_hist | Histogram of missing values per sample |
| nroot_transform | nth root transform |
| ontology_cache | ontology cache |
| OPLSDA | Orthogonal Partial Least Squares regression |
| OPLSR | Orthogonal Partial Least Squares regression |
| pairs_filter | Pairs filter |
| pareto_scale | Pareto scaling |
| PCA | Principal Component Analysis (PCA) |
| pca_biplot | PCA biplot |
| pca_correlation_plot | PCA correlation plot |
| pca_dstat_plot | d-statistic plot |
| pca_loadings_plot | PCA loadings plot |
| pca_scores_plot | PCA scores plot |
| pca_scree_plot | Scree plot |
| permutation_test | Permutation test |
| permutation_test_plot | permutation_test_plot class |
| permute_sample_order | Permute Sample Order |
| PLSDA | Partial least squares discriminant analysis |
| plsda_feature_importance_plot | PLSDA feature importance summary plot |
| plsda_predicted_plot | PLSDA predicted plot |
| plsda_roc_plot | PLSDA ROC plot |
| PLSR | Partial least squares regression |
| plsr_cook_dist | Cook's distance barchart |
| pls_regcoeff_plot | pls_regcoeff_plot class |
| plsr_prediction_plot | PLSR prediction plot |
| plsr_qq_plot | PLSR QQ plot |
| plsr_residual_hist | PLSR residuals histogram |
| pls_scores_plot | PLSDA scores plot |
| pls_vip_plot | PLSDA VIP plot |
| pqn_norm | Probabilistic Quotient Normalisation (PQN) |
| pqn_norm_hist | PQN coefficient histogram |
| prop_na | Fisher's exact test for missing values |
| resample | Data resampling |
| resample_chart | resample_chart class |
| rsd_filter | RSD filter |
| rsd_filter_hist | RSD histogram |
| r_squared | Coefficient of determination (R-squared) |
| run | Runs an iterator, applying the chosen model multiple times. |
| sb_corr | Signal/batch correction for mass spectrometry data |
| scatter_chart | Group scatter chart |
| split_data | Split data |
| stratified_split | Stratified sampling |
| structToolbox-package | structToolbox: Examples of tools built using the Statistics... |
| SVM | Support Vector Machine Classifier |
| svm_plot_2d | SVM scatter plot |
| tic_chart | Total Ion Count chart. |
| tSNE | tSNE |
| tSNE_scatter | Feature boxplot |
| ttest | t-test |
| vec_norm | Vector normalisation |
| wilcox_p_hist | Histogram of p values |
| wilcox_test | wilcoxon signed rank test |
