lsea: Lipid set enrichment analysis (LSEA)

In ahmohamed/lipidr: Data Mining and Analysis of Lipidomics Datasets

Lipid set enrichment analysis (LSEA)

Description

Lipid set enrichment analysis (LSEA)

Usage

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"
)

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 enrichment.
...	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.
annotation	Which lipid set collection to plot.

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_enrichment returns a ggplot object.

Functions

• 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.

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
)
sig_lipidsets <- significant_lipidsets(enrich_results)
plot_enrichment(de_results, sig_lipidsets, annotation="class")
plot_enrichment(de_results, sig_lipidsets, annotation="length")

ahmohamed/lipidr documentation built on July 7, 2023, 2:22 a.m.