GO_enrichment_analysis {GeneSelectR}

Perform gene set enrichment analysis using clusterProfiler

Description

This function performs gene set enrichment analysis on a list of gene sets extracted from an AnnotatedGeneLists object.

Usage

GO_enrichment_analysis(
  annotated_gene_lists,
  list_type = "inbuilt",
  background = NULL,
  organism = "org.Hs.eg.db",
  keyType = "ENTREZID",
  ont = "BP",
  pvalueCutoff = 0.05,
  qvalueCutoff = 0.2,
  pAdjMethod = "fdr",
  ...
)

Arguments

annotated_gene_lists

An AnnotatedGeneLists object containing a list of GeneList objects.

list_type

A type of AnnotatedGeneList from annotate_gene_lists function. Either 'inbuilt' or 'permutation'. (default: 'inbuilt')

background

A character vector representing the background gene set.

organism

A character string corresponding to the organism of interest. Default: "org.Hs.eg.db" (for human).

keyType

A character string indicating the type of gene identifiers. Default: "ENTREZID".

ont

A character string representing GO term ontology. Default: "BP" (for Biological Process).

pvalueCutoff

A numeric value specifying the significance cutoff. Default: 0.05.

qvalueCutoff

A numeric value specifying the q-value cutoff. Default: 0.2.

pAdjMethod

A p-value adjustment method. Should be the one from "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none". Default is 'fdr

...

Other parameters to be passed to clusterProfiler::enrichGO function.

Value

A list containing the enrichment results for each gene set. Each element in the list is named after a gene set and contains an object produced by the enrichGO function from clusterProfiler. This object includes various details about the enrichment analysis, such as enriched GO terms, their associated p-values, q-values, and other relevant statistics. The list excludes results for the "background" gene set, focusing only on the gene sets of interest.

References

To use clusterProfiler in published research, please cite: Yu G, Wang LG, Han Y, He QY. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012;16(5):284-287. doi:10.1089/omi.2011.0118.

Examples

# Creating a mock AnnotatedGeneLists object
gene_symbols <- c("GENE1", "GENE2", "GENE3")
ensembl_ids <- c("ENSG000001", "ENSG000002", "ENSG000003")
entrez_ids <- c("1001", "1002", "1003")

create_mock_gene_list <- function() {
  new("GeneList",
       SYMBOL = gene_symbols,
       ENSEMBL = ensembl_ids,
       ENTREZID = entrez_ids)
}

mock_gene_list1 <- create_mock_gene_list()
mock_gene_list2 <- create_mock_gene_list()

annotated_gene_lists <- new("AnnotatedGeneLists",
                            inbuilt = list(Lasso = mock_gene_list1,
                                           Univariate = mock_gene_list2),
                            permutation = list(Lasso = mock_gene_list1,
                                               Univariate = mock_gene_list2))

# Define a background gene set
background <- c("GENE1", "GENE2", "GENE3")

# Perform GO enrichment analysis
results <- GO_enrichment_analysis(annotated_gene_lists,
                                  background = background,
                                  organism = "org.Hs.eg.db",
                                  keyType = "SYMBOL")
print(results)