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 |