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Run a single hypergeometric test.

rs_hypergeom_test.Rd

Given a set of target genes, this is a Rust implementation of an hypergeometric test testing for overenrichment of the target genes in the 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(
  target_genes,
  gene_sets,
  gene_universe,
  min_overlap,
  fdr_threshold
)

Arguments

target_genes

String vector. Represents the target gene set.

gene_sets

List. Contains the strings that represent the gene sets to test against.

gene_universe

String vector. The features 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

  • odds_ratios - The calculated odds ratios

  • hits - The size of the overlap

  • gene_set_lengths - The length of the gene sets.

  • fdr - The FDR calculated across the gene sets.

  • to_keep - Indices of the gene sets that passed (optional) thresholds.