# Data Mining and Analysis of Lipidomics Datasets

## Documentation for package ‘lipidr’ version 2.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

lipidr-package | Analysis workflow for targeted lipidomics
.LipidomicsExperiment | LipidomicsExperiment object
add_sample_annotation | Add sample annotation to Skyline data frame
annotate_lipids | Parse molecule names to extract lipid class and chain information.
as_lipidomics_experiment | Convert data.frame/matrix to LipidomicsExperiment
data_normalized | Example dataset (normalized and log2 transformed)
de_analysis | Differential analysis of lipids between sample groups
de_design | Differential analysis of lipids between sample groups
fetch_mw_study | Metabolomics Workbench integration
filter_by_cv | Remove molecules with CV larger that a threshold
gen_lipidsets | Generate lipid sets from lipid molecule names
is_logged | Functions to get and set attributes of LipidomicsExperiment objects
is_normalized | Functions to get and set attributes of LipidomicsExperiment objects
is_summarized | Functions to get and set attributes of LipidomicsExperiment objects
lipidDefaults | Default values for lipidr internal functions A set of default mappings and annotation used internally to correctly parse lipid molecule names.
lipidnames_pattern | Patterns used in parsing lipid names
LipidomicsExperiment | Constructor for Lipidomics experiment from list of assays
LipidomicsExperiment-class | LipidomicsExperiment object
lipidr | Analysis workflow for targeted lipidomics
lipidr-data | Description of lipidr datasets
list_mw_studies | Metabolomics Workbench integration
lsea | Lipid set enrichment analysis (LSEA)
mva | Perform multivariate analyses to investigate sample clustering
non_parsed_molecules | Get a list of molecules that couldn't be parsed by 'lipidr'
normalize_istd | Normalize each class by its corresponding internal standard(s).
normalize_pqn | Perform Probabilistic Quotient Normalization for intensities.
plot_chain_distribution | Plot logFC of lipids per class showing chain information
plot_class_enrichment | Lipid set enrichment analysis (LSEA)
plot_heatmap | Plot an annotated heatmap Plots a hierarchically clustered heatmap showing selected sample and lipid molecule annotations.
plot_lipidclass | Informative plots to investigate lipid classes
plot_molecules | Informative plots to investigate individual lipid molecules
plot_mva | Perform multivariate analyses to investigate sample clustering
plot_mva_loadings | Perform multivariate analyses to investigate sample clustering
plot_results_volcano | Differential analysis of lipids between sample groups
plot_samples | Informative plots to investigate samples
plot_trend | Plot a regulation trend line between logFC and chain annotation
read_mwTab | Metabolomics Workbench integration
read_mw_datamatrix | Metabolomics Workbench integration
read_skyline | Read Skyline exported files
remove_non_parsed_molecules | Remove molecules that couldn't be parsed by 'lipidr' from the dataset
set_logged | Functions to get and set attributes of LipidomicsExperiment objects
set_normalized | Functions to get and set attributes of LipidomicsExperiment objects
set_summarized | Functions to get and set attributes of LipidomicsExperiment objects
significant_lipidsets | Lipid set enrichment analysis (LSEA)
significant_molecules | Differential analysis of lipids between sample groups
summarize_transitions | Summarize transitions
top_lipids | Perform multivariate analyses to investigate sample clustering
update_molecule_names | Rename molecules in a dataset.
use_interactive_graphics | Activate interactive graphics