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Reactome pathway over-representation analysis (ORA)

gly_enrich_reactome.Rd

[Deprecated]

This function was deprecated because we decided to move all enrichment analysis functions to the separate glyfun package, which has more features and better API design.

Perform Reactome pathway ORA for protein UniProt accessions using ReactomePA::enrichPathway().

  • gly_enrich_reactome() accepts a glyexp::experiment() and extracts protein information from the "protein" column in the variable information tibble.

  • gly_enrich_reactome_() accepts a character vector of UniProt IDs.

As ReactomePA::enrichPathway() only accepts Entrez IDs, the UniProt IDs will be first transformed into Entrez IDs with clusterProfiler::bitr().

Usage

gly_enrich_reactome(
  exp,
  add_info = TRUE,
  orgdb = "org.Hs.eg.db",
  organism = "human",
  universe = NULL,
  p_adj_method = "BH",
  p_cutoff = 0.05,
  q_cutoff = 0.2
)

gly_enrich_reactome_(
  proteins,
  orgdb = "org.Hs.eg.db",
  organism = "human",
  universe = NULL,
  p_adj_method = "BH",
  p_cutoff = 0.05,
  q_cutoff = 0.2
)

Arguments

exp

(Only for gly_enrich_reactome()) A glyexp::experiment() object.

add_info

A logical value. This parameter is included for API consistency but has no effect since enrichment results do not contain variable or sample columns. Only applicable to top-level APIs.

orgdb

Passed to OrgDb of clusterProfiler::bitr(). Organism database name (e.g., "org.Hs.eg.db" for human). Defaults to "org.Hs.eg.db".

organism

Passed to organism of ReactomePA::enrichPathway(). Species name (e.g., "human", "mouse", "rat"). Defaults to "human".

universe

Background genes. If a character vector, directly passed to universe of ReactomePA::enrichPathway(). You can also provide a glyexp::experiment() object with "glycoproteomics" type. In this case all detected proteins in this experiment will be extracted and passed to universe of ReactomePA::enrichPathway().

p_adj_method

Passed to pAdjustMethod of ReactomePA::enrichPathway().

p_cutoff

Passed to pvalueCutoff of ReactomePA::enrichPathway().

q_cutoff

Passed to qvalueCutoff of ReactomePA::enrichPathway().

proteins

(Only for gly_enrich_reactome_()) A character vector of UniProt accession IDs.

Value

A list with three elements:

  • tidy_result: A tibble with enrichment results containing the following columns:

    • id: Term ID (e.g., R-HSA-XXXXXX)

    • description: Term description

    • gene_ratio: Ratio of genes in the term to total genes in the input

    • bg_ratio: Ratio of genes in the term to total genes in the background

    • p_val: Raw p-value from hypergeometric test

    • p_adj: Adjusted p-value

    • q_value: Q-value (FDR)

    • gene_id: Gene IDs in the term (separated by "/")

    • count: Number of genes in the term

  • raw_result: The raw ReactomePA enrichPathway result object

  • meta_data (only for gly_enrich_reactome()): A list containing metadata from the input experiment The list has classes glystats_reactome_ora_res and glystats_res.

Required packages

These functions require the following packages to be installed:

  • clusterProfiler for ID conversion

  • ReactomePA for enrichment analysis

  • org.Hs.eg.db for human gene annotation or other OrgDb packages

See also

ReactomePA::enrichPathway()