Lipid set enrichment analysis (LSEA)

lsea(
de.results,
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(). Statistic used to rank the lipid list. Default is logFC. Minimum number of molecules in a set to be included in enrichment. Extra parameters passed to fgsea::fgsea(). Output of lsea(). Significance threshold. Default is 0.05. Minimum number of lipids in a set tested for enrichment. Default is 2. List of significantly changed lipid sets (output of significant_lipidsets()). 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: You are trying to run fgseaSimple. It is recommended to use fgseaMultilevel. To run fgseaMultilevel, you need to remove the nperm argument in the fgsea function call.#> 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)