Man pages for ahmohamed/lipidr
Data Mining and Analysis of Lipidomics Datasets
| add_sample_annotation | Add sample annotation to Skyline data frame |
| annotate_lipids | Parse molecule names to extract lipid class and chain... |
| 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 |
| 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 |
| lipidDefaults | Default values for lipidr internal functions A set of default... |
| lipidnames_pattern | Patterns used in parsing lipid names |
| LipidomicsExperiment | Constructor for Lipidomics experiment from list of assays |
| LipidomicsExperiment-class | LipidomicsExperiment object |
| lipidr-data | Description of lipidr datasets |
| lipidr-package | Analysis workflow for targeted lipidomics |
| lsea | Lipid set enrichment analysis (LSEA) |
| mva | Perform multivariate analyses to investigate sample... |
| mw | Metabolomics Workbench integration |
| non_parsed_molecules | Get a list of molecules that couldn't be parsed by 'lipidr' |
| normalize_istd | Normalize each class by its corresponding internal... |
| normalize_pqn | Perform Probabilistic Quotient Normalization for intensities. |
| pipe | Pipe operator |
| plot_chain_distribution | Plot logFC of lipids per class showing chain information |
| plot_lipidclass | Informative plots to investigate lipid classes |
| plot_molecules | Informative plots to investigate individual lipid molecules |
| plot_samples | Informative plots to investigate samples |
| plot_trend | Plot a regulation trend line between logFC and chain... |
| read_skyline | Read Skyline exported files |
| remove_non_parsed_molecules | Remove molecules that couldn't be parsed by 'lipidr' from the... |
| set_attr | Functions to get and set attributes of LipidomicsExperiment... |
| summarize_transitions | Summarize transitions |
| update_molecule_names | Rename molecules in a dataset. |
| use_interactive_graphics | Activate interactive graphics |
