Run selection-bias-aware enrichment with goseq

Usage

enrich_goseq(
  selected,
  genome,
  id,
  bias = NULL,
  gene_to_category = NULL,
  categories = c("GO:CC", "GO:BP", "GO:MF"),
  method = "Wallenius",
  repetitions = 2000,
  include_uncategorized = FALSE,
  plot_fit = FALSE
)

Arguments

selected: Named binary or logical vector over all tested genes.
genome: Genome identifier accepted by goseq::nullp().
id: Gene identifier type accepted by goseq::nullp().
bias: Optional named or position-aligned numeric bias, usually gene length or expression abundance.
gene_to_category: Optional gene-to-category mapping.
categories: GO/KEGG categories passed as test.cats.
method: Enrichment method. Wallenius is the backend recommendation.
repetitions: Sampling repetitions, used only by the sampling method.
include_uncategorized: Include genes without category annotations.
plot_fit: Plot the probability-weighting function for review.

Value

The native enrichment data frame returned by goseq::goseq().