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Run ORA branch of enrichment analysis

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

Loads the cached chemical->gene-symbol mapping, maps Entrez IDs to symbols, runs ORA, and merges chemical names.

Usage

.run_ora(
  x,
  chemicals_meta,
  cache_dir,
  pAdjustMethod,
  interaction_types = NULL,
  gene_id_type = "symbol",
  universe = NULL,
  alpha = NULL,
  alpha_column = NULL,
  ...
)

Arguments

x

Data frame with column EntrezID.

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 used to build the TERM2GENE table and reported in the EnrichedGenes column.

universe

Background gene identifiers, or NULL for all genes in the gene sets. Converted to match gene_id_type, so Entrez IDs may be supplied whichever mode is in use.

alpha

Significance threshold, or NULL. When given, x is taken to be the whole result table: the rows below the threshold are tested and every row is the background.

alpha_column

Column alpha applies to: a name, an index, or NULL for the second column.

...

Forwarded to ora (minGSSize, maxGSSize).

Value

A data frame of ORA enrichment results.