Package index • notame

Tabular data preprocessing

mark_nas(): Mark specified values as missing

flag_detection(): Flag features with low detection rate

flag_contaminants(): Flag contaminants based on blanks

correct_drift(): Correct drift using cubic spline

ruvs_qc(): Remove Unwanted Variation (RUV) between batches

pca_bhattacharyya_dist(): Bhattacharyya distance between batches in PCA space

perform_repeatability(): Compute repeatability measures

assess_quality(): Assess quality information of features

quality(): Extract quality information of features

flag_quality flag_quality(): Flag low-quality features

flag_report(): A report of flagged features

impute_rf(): Impute missing values using random forest

impute_simple(): Simple imputation

cluster_features(): Cluster correlated features originating from the same metabolite

compress_clusters(): Compress clusters of features to a single feature

pqn_normalization(): Probabilistic quotient normalization

inverse_normalize(): Inverse-rank normalization

Preprocessing visualizations

save_QC_plots(): Write all relevant pretreatment visualizations to pdf (from notameViz)

plot_injection_lm(): Estimate the magnitude of drift (from notameViz)

plot_sample_boxplots(): Plot a boxplot for each sample (from notameViz)

plot_dist_density(): Plot distance density (from notameViz)

plot_tsne(): t-SNE scatter plot (from notameViz)

plot_pca(): PCA scatter plot (from notameViz)

plot_tsne_arrows(): t-SNE plot with arrows (from notameViz)

plot_pca_arrows(): PCA plot with arrows (from notameViz)

plot_tsne_hexbin(): t-SNE hexbin plot (from notameViz)

plot_pca_hexbin(): PCA hexbin plot (from notameViz)

plot_dendrogram(): Sample dendrogram (from notameViz)

plot_sample_heatmap(): Sample heatmap (from notameViz)

plot_pca_loadings(): PCA loadings plot (from notameViz)

plot_quality(): Plot quality metrics (from notameViz)

save_batch_plots(): Save batch correction plots (from notameViz)

save_dc_plots(): Save drift correction plots (from notameViz)

visualize_clusters(): Visualize clusters of features (from notameViz)

Feature selection

Univariate analysis

perform_lm(): Linear models (from notameStats)

perform_logistic(): Logistic regression (from notameStats)

perform_lmer(): Linear mixed models (from notameStats)

perform_oneway_anova(): Welch's ANOVA and classic ANOVA (from notameStats)

perform_lm_anova(): Linear models ANOVA table (from notameStats)

perform_t_test(): Pairwise and paired t-tests (from notameStats)

perform_kruskal_wallis(): Kruskal-Wallis rank-sum test (from notameStats)

perform_non_parametric(): Pairwise and paired non-parametric tests (from notameStats)

perform_correlation_tests(): Correlation test (from notameStats)

perform_auc(): Area under curve (from notameStats)

perform_homoscedasticity_tests(): Test homoscedasticity (from notameStats)

cohens_d(): Cohen's D (from notameStats)

fold_change(): Fold change (from notameStats)

summary_statistics(): Summary statistics (from notameStats)

summarize_results(): Statistics cleaning (from notameStats)

Multivariate analysis

fit_rf(): Fit Random Forest (from notameStats)

importance_rf(): Feature importance in random forest (from notameStats)

mixomics_pls() mixomics_pls_optimize() mixomics_spls_optimize(): PLS (from notameStats)

mixomics_pls() mixomics_pls_optimize() mixomics_spls_optimize(): PLS (from notameStats)

mixomics_pls() mixomics_pls_optimize() mixomics_spls_optimize(): PLS (from notameStats)

mixomics_plsda() mixomics_plsda_optimize() mixomics_splsda_optimize(): PLS-DA (from notameStats)

mixomics_plsda() mixomics_plsda_optimize() mixomics_splsda_optimize(): PLS-DA (from notameStats)

Feature-wise visualizations

save_beeswarm_plots(): Save beeswarm plots of each feature by group (from notameViz)

save_group_boxplots(): Save box plots of each feature by group (from notameViz)

save_scatter_plots(): Save scatter plots of each feature against a set variable (from notameViz)

save_subject_line_plots(): Save line plots with mean (from notameViz)

save_group_lineplots(): Save line plots with errorbars by group (from notameViz)

Results visualizations

plot_p_histogram(): Histogram of p-values (from notameViz)

volcano_plot(): Volcano plot (from notameViz)

manhattan_plot(): Manhattan plot (from notameViz)

mz_rt_plot(): Plot m/z vs retention time plot (cloud plot) (from notameViz)

plot_effect_heatmap(): Heatmap of effects between variables, such as correlations (from notameViz)

Object utilities

import_from_excel(): Read formatted Excel files

write_to_excel(): Write results to Excel file

flag() `flag<-`(): Get and set the values in the flag column

drop_flagged(): Drop flagged features

drop_qcs(): Drop QC samples

join_rowData(): Join new columns to feature data

join_colData(): Join new columns to pheno data

combined_data(): Retrieve both sample information and features

merge_notame_sets(): Merge SummarizedExperiment objects together

fix_object(): Fix object for functioning of notame

Other utilities

citations(): Show citations

init_log(): Initialize log to a file

log_text(): Log text to the current log file

finish_log(): Finish a log

fix_MSMS(): Transform the MS/MS output to publication ready

Datasets

toy_notame_set hilic_neg_sample hilic_pos_sample rp_neg_sample rp_pos_sample: Toy data set

Package

notame notame-package: notame package.