# Lipidomics Analysis Workflow in R

## Documentation for package ‘lipidr’ version 1.0.0

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

## Help Pages

lipidr-package | Analysis workflow for targeted lipidomics
.as_regex | Regex-escaping for character vectors.
.read_skyline_file | Internal method to read skyline file
.SkylineExperiment | SkylineExperiment object
add_sample_annotation | Add sample annotation to Skyline data frame
annotate_lipids | Parse molecule names to extract lipid class and chain information.
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
gen_lipidsets | Generate lipid sets from lipid molecule names
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
lipidr | Analysis workflow for targeted lipidomics
lipidr-data | Description of lipidr datasets
lsea | Lipid set enrichment analysis (LSEA)
mva | Perform multivariate analyses to investigate sample clustering
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 a chart of (log2) fold changes of lipids per class showing chain lengths and saturations. If multiple molecules with the same total chain length and saturation are present in the dataset, the 'measure' is averaged, and the number of molecules is indicated on the plot.
plot_class_enrichment | Lipid set enrichment analysis (LSEA)
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
read_skyline | Read Skyline exported files
significant_lipidsets | Lipid set enrichment analysis (LSEA)
significant_molecules | Differential analysis of lipids between sample groups
SkylineExperiment | Constructor for Skyline experiment from list of assays
SkylineExperiment-class | SkylineExperiment object
summarize_transitions | Summarize transitions
top_lipids | Perform multivariate analyses to investigate sample clustering
use_interactive_graphics | Activate interactive graphics