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Gene set enrichment (GSE) based on a hypergeometric test.

gse_hypergeometric.Rd

Takes a set of target genes, a list of gene sets and calculates a p-value (hypergeometric test) and odds ratio (OR) against all the gene sets. Also applies a multiple hypothesis correction (BH) to the p-values.

Usage

gse_hypergeometric(
  target_genes,
  gene_set_list,
  gene_universe = NULL,
  threshold = 0.05,
  minimum_overlap = 3L,
  .verbose = FALSE
)

Arguments

target_genes

Character vector. GeneID(s) of the target genes.

gene_set_list

Named list of character vectors. Names should represent the gene sets, pathways, and the elements the genes within the respective gene set.

gene_universe

Optional character vector. If you would like to specify specifically the gene universe. If set to NULL, the function will default to all represented genes in the gene_set_list.

threshold

Float between 0 and 1 to filter on the fdr. Default: 0.05. If 1 everything is returned.

minimum_overlap

Number of minimum overlap between the target genes and the respective gene set.

.verbose

Boolean. Controls verbosity of the function.

Value

data.table with enrichment results.