Skip to contents

Run hypergeometric enrichment over the gene ontology

rs_gse_geom_elim.Rd

This function implements a Rust version of the gene ontology enrichment with elimination: the starting point are the leafs of the ontology and hypergeometric tests will first conducted there. Should the hypergeometric test p-value be below a certain threshold, the genes of that gene ontology term will be removed from all ancestors. WARNING! Incorrect use can cause kernel crashes. Wrapper around the Rust functions with type checks are provided in the package.

Usage

rs_gse_geom_elim(
  target_genes,
  levels,
  go_obj,
  gene_universe_length,
  min_genes,
  elim_threshold,
  min_overlap,
  fdr_threshold
)

Arguments

target_genes

A character vector representing the target gene set.

levels

A character vector representing the levels to iterate through. The order will be the one the iterations are happening in.

go_obj

The gene_ontology_data S7 class. See gene_ontology_data().

gene_universe_length

The length of the gene universe.

min_genes

number of minimum genes for the gene ontology term to be tested.

elim_threshold

p-value below which the elimination procedure shall be applied to the ancestors.

min_overlap

Optional minimum overlap threshold.

fdr_threshold

Optional fdr threshold.

Value

A list containing:

  • go_ids - The gene ontology identifier.

  • pvals - The calculated odds ratios.

  • odds_ratios - The calculated odds ratios.

  • overlap - The size of the overlap.

  • gene_set_lengths - The length of the gene sets.