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Run a hypergeometric test over a list of target genes

rs_hypergeom_test_list.Rd

Given a list of target gene sets, this function will test for each of the individual target genes the hypergeoemetric enrichment against the specified gene sets. WARNING! Incorrect use can cause kernel crashes. Wrapper around the Rust functions with type checks are provided in the package.

Usage

rs_hypergeom_test_list(
  target_genes_list,
  gene_sets,
  gene_universe,
  min_overlap,
  fdr_threshold
)

Arguments

target_genes_list

A character vector representing the target gene set.

gene_sets

A list of strings that represent the gene sets to test against.

gene_universe

A character vector representing the gene universe from which the target genes and gene sets are sampled from.

min_overlap

Optional integer. Shall a filter be applied on the minimum of overlappign genes.

fdr_threshold

Optional float. Shall a filter be applied for the maximum tolerated FDR.

Value

A list containing:

  • pvals - The p-values from the hypergeometric test.

  • fdr - The FDRs for each target gene calculated across all gene sets.

  • odds ratios - The calculated odds ratios

  • hits - The size of the overlap between the target gene set and individual gene sets.

  • gene_set_lengths - The length of the gene sets.

  • to_keep - Indices of the tests that passed.

  • tests_passed - How many tests passed the filter criteria for that target set.