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")

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 enrichemnt. |

... | 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", 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)