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 and normalize lipidomics datasets

summarize_transitions()

Summarize transitions

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()

Lipid set enrichment analysis (LSEA)

gen_lipidsets()

Generate lipid sets from lipid molecule names

Clustring analysis

plot_heatmap()

Plot an annotated heatmap Plots a hierarchically clustered heatmap showing selected sample and lipid molecule annotations.

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 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