Man pages for antonvsdata/notame
Workflow for non-targeted LC-MS metabolic profiling
| align_batches | Align features between batches |
| assess_quality | Assess quality information of features |
| assign_cluster_id | Assign Cluster ID to features |
| citations | Show citations |
| clean_stats_results | Statistics cleaning |
| cluster_features | Cluster correlated features |
| cohens_d | Cohen's D |
| combined_data | Retrieve both sample information and features |
| compress_clusters | Compress clusters of features to a single feature |
| construct_metabosets | Construct MetaboSet objects |
| correct_drift | Correct drift using cubic spline |
| create_feature_plot_list | Generate a list of plots |
| dc_cubic_spline | Fit a cubic spline to correct drift |
| dobc | Batch correction |
| dot-onLoad | Set default color scales on load |
| drop_flagged | Drop flagged features |
| drop_qcs | Drop QC samples |
| example_set | Toy data set |
| exponential | Exponential function |
| find_clusters | Extract the densely connected clusters |
| find_connections | Find out which features are correlated within a specified... |
| finish_log | Finish a log |
| finite_helpers | Summary statistics of finite elements |
| fit_rf | Fit Random Forest |
| fix_MSMS | Transform the MS/MS output to publication ready |
| flag_contaminants | Flag contaminants |
| flag_detection | Flag features with low detection rate |
| flag_quality | Flag low-quality features |
| flag_report | A report of flagged features |
| fold_change | Fold change |
| get_x | A helper function for extracting predictor matrix with... |
| importance_rf | Feature importance in random forest |
| impute_rf | Impute missing values using random forest |
| impute_simple | Simple imputation |
| init_log | Initialize log to a file |
| inspect_dc | Flag the results of drift correction |
| install_dependencies | Install dependencies |
| inverse_normalize | Inverse-rank normalization |
| join_fData | Join new columns to feature data |
| join_pData | Join new columns to pheno data |
| log-MetaboSet-method | Logarithm |
| log_text | Log text to the current log file |
| manhattan_plot | Manhattan plot |
| mark_nas | Mark specified values as missing |
| mark_qcs | Replace NA values in pheno data columns with "QC" |
| merge_batches | DEPRECATED: Merge MetaboSet objects of batches together |
| merged_sample | Sample dataset |
| merge_exprs | Partially replace exprs field with new values |
| merge_metabosets | Merge MetaboSet objects together |
| MetaboSet-class | An S4 class used to represent LC-MS datasets |
| muvr_analysis | MUVR |
| mz_rt_plot | Plot m/z vs retention time plot |
| normalize_batches | Normalize batches |
| pca_bhattacharyya_dist | Bhattacharyya distance between bathces in PCA space |
| perform_auc | Area under curve |
| perform_correlation_tests | Perform correlation tests |
| perform_homoscedasticity_tests | Test homoscedasticity |
| perform_kruskal_wallis | Perform Kruskal-Wallis Rank Sum Tests |
| perform_lm | Linear models |
| perform_lm_anova | Linear models ANOVA table |
| perform_lmer | Linear mixed models |
| perform_logistic | Logistic regression |
| perform_mann_whitney | Perform Mann-Whitney u test |
| perform_oneway_anova | Perform ANOVA |
| perform_paired_t_test | Perform paired t-tests |
| perform_pairwise_non_parametric | Perform pairwise non-parametric tests |
| perform_pairwise_t_test | Perform pairwise t-tests |
| perform_permanova | Perform PERMANOVA |
| perform_repeatability | Compute repeatability measures |
| perform_t_test | Perform t-tests |
| perform_wilcoxon_signed_rank | Perform Wilcoxon signed rank test |
| plot_dendrogram | Draw dendrograms |
| plot_dist_density | Distance density plot |
| plot_effect_heatmap | Draw a heatmap of effects between variables, such as... |
| plot_injection_lm | Estimate the magnitude of drift |
| plot_pca | PCA scatter plot |
| plot_pca_arrows | PCA plot with arrows |
| plot_pca_hexbin | PCA hexbin plot |
| plot_pca_loadings | PCA loadings plot |
| plot_p_histogram | Histogram of p-values |
| plot_pls | Plot points in PLS space |
| plot_quality | Plot quality metrics |
| plot_sample_boxplots | Plot a boxplot for each sample |
| plot_sample_heatmap | Draw heatmaps |
| plot_sample_suprahex | Suprahex plots |
| plot_tsne | t-SNE scatter plot |
| plot_tsne_arrows | t-SNE plot with arrows |
| plot_tsne_hexbin | t-SNE hexbin plot |
| pls | PLS |
| pls_da | PLS-DA |
| pqn_normalization | Probabilistic quotient normalization |
| prop_found | Proportion of non-missing values in a vector |
| prop_na | Proportion of NA values in a vector |
| pull_clusters | Extract information of the features in clusters |
| quality | Extract quality information of features |
| read_from_excel | Read formatted Excel files |
| ruvs_qc | Remove Unwanted Variation |
| save_batch_plots | Save batch correction plots |
| save_beeswarm_plots | Save beeswarm plots of each feature by group |
| save_dc_plots | Drift correction plots |
| save_feature_plots | Save plots of individual features |
| save_group_boxplots | Save box plots of each feature by group |
| save_group_lineplots | Save line plots with errorbars by group |
| save_plot | Save plot to chosen format |
| save_scatter_plots | Save scatter plots of each feature against a set variable |
| save_subject_line_plots | Save line plots with mean |
| scale-MetaboSet-method | Scale exprs data |
| summary_statistics | Summary statistics |
| visualizations | Write all relevant visualizations to pdf |
| visualize_clusters | Visualize clusters of features |
| volcano_plot | Volcano plot |
| write_to_excel | Write results to Excel file |
