Data Mining and Analysis of Lipidomics Datasets

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Documentation for package ‘lipidr’ version 2.8.1

• 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
impute_na	Impute missing values in a LipidomicsExperiment
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_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