Disease enrichment analysis (MIDAS) — query_disease

Perform Fisher's exact test enrichment analysis to identify diseases significantly associated with a gene list.

Usage

query_disease_enrichment(
  gene_list,
  gene_id_type = "symbol",
  sources = NULL,
  min_sources = 1L,
  background_gene_count = 20000L,
  p_value_cutoff = 0.05,
  correction_method = "fdr",
  min_hit_count = 2L,
  page = 1L,
  page_size = 20L
)

Arguments

gene_list: Character vector of gene identifiers.
gene_id_type: ID type: "symbol" (default), "entrez", or "ensembl".
sources: Character vector of source databases (or NULL).
min_sources: Minimum supporting sources (default 1).
background_gene_count: Background gene count (default 20000).
p_value_cutoff: P-value significance cutoff (default 0.05).
correction_method: P-value correction: "fdr" (default), "bonferroni", "holm", or "none".
min_hit_count: Minimum gene hits per disease (default 2).
page: Page number (default 1).
page_size: Results per page (default 20).

Value

A tibble::tibble() of enrichment results with attributes "total_significant", "total_tested", and "input_gene_count".

Examples

if (FALSE) { # \dontrun{
query_disease_enrichment(c("TP53", "BRCA1", "EGFR", "VEGFA"))
} # }