GO enrichment with gene sets — enrichGO

Gene ontology enrichment analysis of multiple gene sets with clusterProfiler, allowing for using different or same background genes for each gene set

Usage

enrichGO_list(
  gene_list,
  keyType = "SYMBOL",
  OrgDb,
  universe = NULL,
  universe_list = NULL,
  pAdjustMethod = "BH",
  pvalueCutoff = 0.05,
  qvalueCutoff = 0.05,
  category = NULL,
  simplify = FALSE,
  simplify_cutoff = 0.7,
  simplify_by = "p.adjust",
  simplify_select_fun = min,
  simplify_measure = "Wang",
  ...
)

Arguments

gene_list: A named list of gene vectors, or a data.frame with Feature and Module columns from WGCNA_module().
keyType: (Optional) Available options are AnnotationDbi::keytypes(OrgDb) (default is "SYMBOL")
OrgDb: Organism database, e.g. org.Hs.eg.db, org.Mm.eg.db
universe: Background genes for all input gene sets, used if universe_list is not provided
universe_list: Background genes for each input gene set, a list of gene vectors with the same names as gene_list
pAdjustMethod: (Optional) Parameter of clusterProfiler::enrichGO() (default is "BH")
pvalueCutoff: (Optional) Parameter of clusterProfiler::enrichGO() (default is 0.05)
qvalueCutoff: (Optional) Parameter of clusterProfiler::enrichGO() (default is 0.05)
category: (Optional) GO category to analyze (default is all three of BP, MF, CC)
simplify: (Optional) Whether to simplify the GO terms by removing redundant terms with clusterProfiler::simplify() function. (default is FALSE)
simplify_cutoff: (Optional) Parameter of clusterProfiler::simplify(), cutoff for similarity when simplifying GO terms (default is 0.7)
simplify_by: (Optional) Parameter of clusterProfiler::simplify(), method to choose representative term when simplifying GO terms (default is "p.adjust")
simplify_select_fun: (Optional) Parameter of clusterProfiler::simplify(), function to select representative term when simplifying GO terms (default is min)
simplify_measure: (Optional) Parameter of clusterProfiler::simplify(), method to calculate similarity when simplifying GO terms (default is "Wang")
...: additional arguments passed to clusterProfiler::enrichGO()

Value

A nested list of GO enrichment results with sublists: 'all' and 'simplified' (if simplify = TRUE) containing merged results of all or simplified terms across gene sets for each GO category; 'unmerged_all' and 'unmerged_simplified' (if simplify = TRUE) including all or simplified terms for each gene set and GO category.

Examples

if (requireNamespace("org.Mm.eg.db", quietly = TRUE)) {
    library(org.Mm.eg.db)
    library(clusterProfiler)
    data(example_net)
    # select two modules for demonstration
    example_module <- WGCNA_module(example_net) |>
        dplyr::filter(Module %in% c("1", "2"))
    # set cutoff to 1 to show all results for demonstration
    example_go_list = enrichGO_list(example_module, OrgDb = org.Mm.eg.db,
        universe = WGCNA_module(example_net, exclude_grey = FALSE)$Feature,
        pvalueCutoff = 1, qvalueCutoff = 1,
        category = "BP", simplify = FALSE)
}
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#> Performing GO enrichment for category: BP
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#> Merging GO enrichment results across gene lists for each category.