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Run hypergeometric enrichment a list of target genes over the gene ontology

rs_gse_geom_elim_list.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. This function is designed to leverage Rust-based threading for parallel processing of a list of target genes. 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_list(
  target_genes_list,
  levels,
  go_obj,
  gene_universe_length,
  min_genes,
  elim_threshold,
  min_overlap,
  fdr_threshold
)

Arguments

target_genes_list

A list of target genes against which to run the method.

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.

  • fdrs - The calculated fdrs.

  • odds_ratios - The calculated odds ratios.

  • overlap - The size of the overlap.

  • gene_set_lengths - The length of the gene sets.

  • no_test - The number of tests for that target set that passed the thresholds.