Smoothing Metabolomics Analyses

align_batches | Align features between batches |

assign_cluster_id | Assign Cluster ID to features |

autoplot.lmerMod | Autoplot 'lme4::lmerMod' |

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_MetaboSet | Construct MetaboSet objects |

correct_drift | Correct drift using cubic spline |

dc_cubic_spline | Fit a cubic spline to correct drift |

dobc | Batch correction |

drop_flagged | Drop flagged features |

drop_qcs | Drop QC samples |

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 |

flag | Extract flags of features |

flag_detection | Flag features with low detection rate |

flag_quality | Flag low-quality features |

flag_report | A report of flagged features |

flatten | Flatten dataframe contains matrix |

fold_change | Fold change |

geom_factory | Factory function to control 'ggplot2::geom_xxx' functions |

get.layout | Calcurate layout matrix for 'ggmultiplot' |

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 |

inverse_normalize | Inverse-rank normalization |

join_fData | Join new columns to feature data |

join_results | Join results to a MetaboSet object |

log-MetaboSet-method | Logarithm |

log_state | Get the current logging state |

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 | Merge MetaboSet objects of batches together |

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 |

mixomics_plsda | PLS-DA |

mixomics_plsda_optimize | PLS-DA |

mixomics_splsda_optimize | sPLS-DA |

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_lmer | Linear mixed models |

perform_logistic | Logistic regression |

perform_oneway_anova | Perform ANOVA |

perform_pairwise_t_test | Perform pairwise t-tests |

perform_repeatability | Compute repeatability measures |

perform_t_test | Perform t-tests |

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_label | Attach label to 'ggplot2::ggplot' |

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_quality | Plot quality metrics |

plot_sample_boxplots | Plot a boxplot for each sample |

plot_sample_heatmap | Draw heatmaps |

plot_tsne | t-SNE scatter plot |

plot_tsne_arrows | t-SNE plot with arrows |

plot_tsne_hexbin | t-SNE hexbin plot |

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 |

read_from_excel | Read formatted Excel files |

ruvs_qc | Remove Unwanted Variation |

save_batch_plots | Save batch correction plots |

save_dc_plots | Drift correction plots |

save_group_boxplots | Save box plots of each feature by group |

save_group_lineplots | Save line plots with errorbars by group |

save_lm_diagnostic_plots | Plot model diagnostics |

save_plot | Save plot to PDF |

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 |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.