Data Mining and Analysis of Lipidomics Datasets
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Documentation for package ‘lipidr’ version 2.22.1
Help Pages
| .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 |
| 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 |
| LipidomicsExperiment | Constructor for Lipidomics experiment from list of assays |
| LipidomicsExperiment-class | LipidomicsExperiment object |
| 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_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 |