Description Usage Arguments Value Functions Examples
Lipid set enrichment analysis (LSEA)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17  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")
plot_enrichment(
de.results,
significant.sets,
annotation = c("class", "length", "unsat"),
measure = "logFC"
)

de.results 
Output of 
rank.by 
Statistic used to rank the lipid list. Default is 
min_size 
Minimum number of molecules in a set to be included in enrichment. 
... 
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 
annotation 
Which lipid set collection to plot. 
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_enrichment
returns a ggplot object.
significant_lipidsets
: gets a list of significantly changed lipid sets
plot_enrichment
: is usually used to look at log2 fold change
distribution of lipids in each class, chain length or unsaturation,
marking significantly enriched sets. It can also be used to plot P.Value
or Adj.P.Val
.
1 2 3 4 5 6 7 8 9 10 11 12 13  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
)
sig_lipidsets < significant_lipidsets(enrich_results)
plot_enrichment(de_results, sig_lipidsets, annotation="class")
plot_enrichment(de_results, sig_lipidsets, annotation="length")

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