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WikiPathways over-representation analysis (ORA)

gly_enrich_wikipathways.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 WikiPathways ORA for protein UniProt accessions using clusterProfiler::enrichWP().

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

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

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

Usage

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

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

Arguments

exp

(Only for gly_enrich_wikipathways()) 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.

organism

Passed to organism of clusterProfiler::enrichWP(). Species name (e.g., "Homo sapiens", "Mus musculus", "Rattus norvegicus"). Defaults to "Homo sapiens".

orgdb

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

universe

Background genes. If a character vector, it is expected to contain UniProt accession IDs; these will be converted to Entrez Gene IDs and then passed to universe of clusterProfiler::enrichWP(). You can also provide a glyexp::experiment() object with "glycoproteomics" type. In this case all detected proteins in this experiment will be extracted as UniProt IDs, converted to Entrez IDs, and then passed to universe of clusterProfiler::enrichWP().

p_adj_method

Passed to pAdjustMethod of clusterProfiler::enrichWP().

p_cutoff

Passed to pvalueCutoff of clusterProfiler::enrichWP().

q_cutoff

Passed to qvalueCutoff of clusterProfiler::enrichWP().

proteins

(Only for gly_enrich_wikipathways_()) 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., WPXXXXX)

    • 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 clusterProfiler enrichResult object

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

Required packages

These functions require the following packages to be installed:

  • clusterProfiler for enrichment analysis and ID conversion

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

See also

clusterProfiler::enrichWP()