Skip to contents

Run GSEA branch of enrichment analysis

Source: R/enrichment_analysis.R
dot-run_gsea.Rd

Loads the cached chemical->Entrez-ID mapping, prepares the ranked input, calls the gsea engine, and feeds the result through the shared .format_enrichment_result.

Usage

.run_gsea(
  x,
  chemicals_meta,
  cache_dir,
  pAdjustMethod,
  interaction_types = NULL,
  gene_id_type = "symbol",
  ...
)

Arguments

x

Data frame with column EntrezID and a numeric value column used for ranking.

chemicals_meta

Data frame with ChemicalID and ChemicalName columns.

cache_dir

Directory holding cached CTD .rda files.

pAdjustMethod

Multiple-testing correction name.

interaction_types

Character vector of CTD InteractionActions values to retain when building gene sets, or NULL for all.

gene_id_type

Either "symbol" or "entrez": the identifier reported in the EnrichedGenes column.

...

Forwarded to gsea (e.g. minSize, maxSize).

Value

A data frame of GSEA enrichment results, formatted by .format_enrichment_result.