Man pages for ahmohamed/lipidr
Data Mining and Analysis of Lipidomics Datasets

add_sample_annotationAdd sample annotation to Skyline data frame
annotate_lipidsParse molecule names to extract lipid class and chain...
as_lipidomics_experimentConvert data.frame/matrix to LipidomicsExperiment
data_normalizedExample dataset (normalized and log2 transformed)
de_analysisDifferential analysis of lipids between sample groups
filter_by_cvRemove molecules with CV larger that a threshold
gen_lipidsetsGenerate lipid sets from lipid molecule names
impute_naImpute missing values in a LipidomicsExperiment
lipidDefaultsDefault values for lipidr internal functions A set of default...
lipidnames_patternPatterns used in parsing lipid names
LipidomicsExperimentConstructor for Lipidomics experiment from list of assays
LipidomicsExperiment-classLipidomicsExperiment object
lipidr-dataDescription of lipidr datasets
lipidr-packageAnalysis workflow for targeted lipidomics
lseaLipid set enrichment analysis (LSEA)
mvaPerform multivariate analyses to investigate sample...
mwMetabolomics Workbench integration
non_parsed_moleculesGet a list of molecules that couldn't be parsed by 'lipidr'
normalize_istdNormalize each class by its corresponding internal...
normalize_pqnPerform Probabilistic Quotient Normalization for intensities.
pipePipe operator
plot_chain_distributionPlot logFC of lipids per class showing chain information
plot_heatmapPlot an annotated heatmap Plots a hierarchically clustered...
plot_lipidclassInformative plots to investigate lipid classes
plot_moleculesInformative plots to investigate individual lipid molecules
plot_samplesInformative plots to investigate samples
plot_trendPlot a regulation trend line between logFC and chain...
read_skylineRead Skyline exported files
remove_non_parsed_moleculesRemove molecules that couldn't be parsed by 'lipidr' from the...
set_attrFunctions to get and set attributes of LipidomicsExperiment...
summarize_transitionsSummarize transitions
update_molecule_namesRename molecules in a dataset.
use_interactive_graphicsActivate interactive graphics
ahmohamed/lipidr documentation built on Aug. 17, 2022, 1:35 a.m.