lsea {lipidr} | R Documentation |
Lipid set enrichment analysis (LSEA)
lsea(de.results, rank.by = c("logFC", "P.Value", "Adj.P.Val"), ...) significant_lipidsets(enrich.results, p.cutoff = 0.05, size.cutoff = 2) plot_class_enrichment(de.results, significant.sets, measure = "logFC")
de.results |
Output of |
rank.by |
Statistic used to rank the lipid list. Default is |
... |
Extra parameters passed to |
enrich.results |
Output of |
p.cutoff |
Significance threshold. Default is |
size.cutoff |
Minimum number of lipids in a set tested for enrichment.
Default is |
significant.sets |
List of significantly changed lipid sets
(output of |
measure |
Which measure to plot the distribution of: logFC, P.Value,
Adj.P.Val. Default is |
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.
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
.
data(data_normalized) de_results <- de_analysis( data_normalized, HighFat_water - NormalDiet_water, measure = "Area" ) enrich_results <- lsea( de_results, rank.by = "logFC", minSize = 4, nperm = 1000 ) sig_lipidsets <- significant_lipidsets(enrich_results) plot_class_enrichment(de_results, sig_lipidsets)