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 |
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