Files in antonvsdata/notame

Workflow for non-targeted LC-MS metabolic profiling

R/batch_correction.R R/class_constructor.R R/cluster_plots.R R/data.R R/drift_correction.R R/effect_heatmap.R R/effect_plots.R R/feature_clustering.R R/logging.R R/merger.R R/multivariate.R R/qc_visualizations.R R/quality_metrics.R R/scatter.R R/stats.R R/suprahex_plots.R R/transformations.R R/utils.R R/visualization_utils.R README.md data-raw/example_data.R data-raw/sample_data.R inst/doc/MetaboSet.R inst/doc/MetaboSet.Rmd inst/doc/feature_clustering.R inst/doc/feature_clustering.Rmd inst/doc/intro.R inst/doc/intro.Rmd inst/doc/preprocessing.R inst/doc/preprocessing.Rmd inst/doc/project_example.R inst/doc/project_example.Rmd inst/doc/project_template.R inst/doc/project_template.Rmd inst/doc/statistics.R inst/doc/statistics.Rmd inst/doc/visualizations.R inst/doc/visualizations.Rmd man/MetaboSet-class.Rd man/align_batches.Rd man/assess_quality.Rd man/assign_cluster_id.Rd man/citations.Rd man/clean_stats_results.Rd man/cluster_features.Rd man/cohens_d.Rd man/combined_data.Rd man/compress_clusters.Rd man/construct_metabosets.Rd man/correct_drift.Rd man/create_feature_plot_list.Rd man/dc_cubic_spline.Rd man/dobc.Rd man/dot-onLoad.Rd man/drop_flagged.Rd man/drop_qcs.Rd man/example_set.Rd man/exponential.Rd man/find_clusters.Rd man/find_connections.Rd man/finish_log.Rd man/finite_helpers.Rd man/fit_rf.Rd man/fix_MSMS.Rd man/flag_contaminants.Rd man/flag_detection.Rd man/flag_quality.Rd man/flag_report.Rd man/fold_change.Rd man/get_x.Rd man/importance_rf.Rd man/impute_rf.Rd man/impute_simple.Rd man/init_log.Rd man/inspect_dc.Rd man/install_dependencies.Rd man/inverse_normalize.Rd man/join_fData.Rd man/join_pData.Rd man/log-MetaboSet-method.Rd man/log_text.Rd man/manhattan_plot.Rd man/mark_nas.Rd man/mark_qcs.Rd man/merge_batches.Rd man/merge_exprs.Rd man/merge_metabosets.Rd man/merged_sample.Rd man/muvr_analysis.Rd man/mz_rt_plot.Rd man/normalize_batches.Rd man/pca_bhattacharyya_dist.Rd man/perform_auc.Rd man/perform_correlation_tests.Rd man/perform_homoscedasticity_tests.Rd man/perform_kruskal_wallis.Rd man/perform_lm.Rd man/perform_lm_anova.Rd man/perform_lmer.Rd man/perform_logistic.Rd man/perform_mann_whitney.Rd man/perform_oneway_anova.Rd man/perform_paired_t_test.Rd man/perform_pairwise_non_parametric.Rd man/perform_pairwise_t_test.Rd man/perform_permanova.Rd man/perform_repeatability.Rd man/perform_t_test.Rd man/perform_wilcoxon_signed_rank.Rd man/plot_dendrogram.Rd man/plot_dist_density.Rd man/plot_effect_heatmap.Rd man/plot_injection_lm.Rd man/plot_p_histogram.Rd man/plot_pca.Rd man/plot_pca_arrows.Rd man/plot_pca_hexbin.Rd man/plot_pca_loadings.Rd man/plot_pls.Rd man/plot_quality.Rd man/plot_sample_boxplots.Rd man/plot_sample_heatmap.Rd man/plot_sample_suprahex.Rd man/plot_tsne.Rd man/plot_tsne_arrows.Rd man/plot_tsne_hexbin.Rd man/pls.Rd man/pls_da.Rd man/pqn_normalization.Rd man/prop_found.Rd man/prop_na.Rd man/pull_clusters.Rd man/quality.Rd man/read_from_excel.Rd man/ruvs_qc.Rd man/save_batch_plots.Rd man/save_beeswarm_plots.Rd man/save_dc_plots.Rd man/save_feature_plots.Rd man/save_group_boxplots.Rd man/save_group_lineplots.Rd man/save_plot.Rd man/save_scatter_plots.Rd man/save_subject_line_plots.Rd man/scale-MetaboSet-method.Rd man/summary_statistics.Rd man/visualizations.Rd man/visualize_clusters.Rd man/volcano_plot.Rd man/write_to_excel.Rd tests/testthat.R tests/testthat/helper.R tests/testthat/test_constructor.R tests/testthat/test_data_reading.R tests/testthat/test_finite_functions.R tests/testthat/test_logging.R tests/testthat/test_plotting.R tests/testthat/test_scatter.R tests/testthat/test_stats.R tests/testthat/test_transformations.R vignettes/MetaboSet.Rmd vignettes/feature_clustering.Rmd vignettes/intro.Rmd vignettes/preprocessing.Rmd vignettes/project_example.Rmd vignettes/project_template.Rmd vignettes/statistics.Rmd vignettes/visualizations.Rmd