Function reference • lipidr

Input data Functions to read and input data in `lipidr`
`read_skyline()`	Read Skyline exported files
`as_lipidomics_experiment()`	Convert data.frame/matrix to LipidomicsExperiment
`add_sample_annotation()`	Add sample annotation to Skyline data frame
`list_mw_studies()` `fetch_mw_study()` `read_mwTab()` `read_mw_datamatrix()`	Metabolomics Workbench integration
Preprocessing data Functions to summarise, impute and normalize lipidomics datasets
`summarize_transitions()`	Summarize transitions
`impute_na()`	Impute missing values in a LipidomicsExperiment
`normalize_istd()`	Normalize each class by its corresponding internal standard(s).
`normalize_pqn()`	Perform Probabilistic Quotient Normalization for intensities.
Quality control and data visualization Functions to visually QC your lipidomics datasets
`plot_lipidclass()`	Informative plots to investigate lipid classes
`plot_molecules()`	Informative plots to investigate individual lipid molecules
`plot_samples()`	Informative plots to investigate samples
`filter_by_cv()`	Remove molecules with CV larger that a threshold
Univariate analysis Perform univariate analysis for lipidomics datasets
`de_analysis()` `de_design()` `significant_molecules()` `plot_results_volcano()`	Differential analysis of lipids between sample groups
Multivariate analysis Perform and visualize PCA, PCoA and OPLS-DA for lipidomics datasets
`mva()` `plot_mva()` `plot_mva_loadings()` `top_lipids()`	Perform multivariate analyses to investigate sample clustering
Enrichment analysis
`lsea()` `significant_lipidsets()` `plot_class_enrichment()` `plot_enrichment()`	Lipid set enrichment analysis (LSEA)
`gen_lipidsets()`	Generate lipid sets from lipid molecule names
Lipid-centric analysis
`plot_chain_distribution()`	Plot logFC of lipids per class showing chain information
`plot_trend()`	Plot a regulation trend line between logFC and chain annotation
`annotate_lipids()`	Parse molecule names to extract lipid class and chain information.
Integration with Metabolomics Workbench for data mining
`list_mw_studies()` `fetch_mw_study()` `read_mwTab()` `read_mw_datamatrix()`	Metabolomics Workbench integration
LipidomicsExperiment object structure and manipulation
`LipidomicsExperiment-class` `.LipidomicsExperiment`	LipidomicsExperiment object
`LipidomicsExperiment()`	Constructor for Lipidomics experiment from list of assays
`is_logged()` `set_logged()` `is_normalized()` `set_normalized()` `is_summarized()` `set_summarized()`	Functions to get and set attributes of LipidomicsExperiment objects
`update_molecule_names()`	Rename molecules in a dataset.
`filter_by_cv()`	Remove molecules with CV larger that a threshold
`non_parsed_molecules()`	Get a list of molecules that couldn't be parsed by `lipidr`
`remove_non_parsed_molecules()`	Remove molecules that couldn't be parsed by `lipidr` from the dataset
Enable interactive graphics
`use_interactive_graphics()`	Activate interactive graphics

Reference

Input data

Preprocessing data

Quality control and data visualization

Univariate analysis

Multivariate analysis

Enrichment analysis

Lipid-centric analysis

Integration with Metabolomics Workbench for data mining

LipidomicsExperiment object structure and manipulation

Enable interactive graphics