Run a hypergeometric test over a list of target genes — rs_hypergeom_test

Given a list of target gene sets, this function will test for each of the individual target gene sets the hypergeometric enrichment against the specified gene sets.

Usage

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

Arguments

target_genes_list: A list of character vectors, each representing a 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 overlapping genes.
fdr_threshold: Optional float. Shall a filter be applied for the maximum tolerated FDR.

Value

A list containing (results of all target sets concatenated, only for the tests passing the filters):

pvals - The p-values from the hypergeometric test.
fdr - The FDRs for each target set 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 - 1-based indices (into gene_sets) of the tests that passed.
tests_passed - How many tests passed the filter criteria for that target set.