Lipid set enrichment analysis (LSEA)

lsea(de.results, rank.by = c("logFC", "P.Value", "adj.P.Val"),
  min_size = 2, ...)

significant_lipidsets(enrich.results, p.cutoff = 0.05, size.cutoff = 2)

plot_class_enrichment(de.results, significant.sets, measure = "logFC")

Arguments

de.results

Output of de_analysis().

rank.by

Statistic used to rank the lipid list. Default is logFC.

min_size

Minimum number of molecules in a set to be included in enrichemnt.

...

Extra parameters passed to fgsea::fgsea().

enrich.results

Output of lsea().

p.cutoff

Significance threshold. Default is 0.05.

size.cutoff

Minimum number of lipids in a set tested for enrichment. Default is 2.

significant.sets

List of significantly changed lipid sets (output of significant_lipidsets()).

measure

Which measure to plot the distribution of: logFC, P.Value, Adj.P.Val. Default is logFC.

Value

lsea returns enrichment results (data.frame) as returned from fgsea::fgsea(). The results also contain the following attributes:

  • de.results Original de.results input.

  • rank.by Measure used to rank lipid molecules.

  • sets Lipid sets tested, with their member molecules.

significant_lipidsets returns a list of character vectors of significantly enriched sets for each contrast.

plot_class_enrichment returns a ggplot object.

Functions

  • significant_lipidsets: gets a list of significantly changed lipid sets

  • plot_class_enrichment: is usually used to look at log2 fold change distribution of lipids in each class, marking significantly enriched classes. Can also be used to plot P.Value or Adj.P.Val.

Examples

data(data_normalized) de_results <- de_analysis( data_normalized, HighFat_water - NormalDiet_water, measure = "Area" ) enrich_results <- lsea( de_results, rank.by = "logFC", min_size = 4, nperm = 1000 )
#> Warning: There are ties in the preranked stats (5.78% of the list). #> The order of those tied genes will be arbitrary, which may produce unexpected results.
sig_lipidsets <- significant_lipidsets(enrich_results) plot_class_enrichment(de_results, sig_lipidsets)