ORA: Classical Over Representation Analysis with FOBI

Description Usage Arguments Value Author(s) References Examples

Description

This function performs a traditional over representation analysis based on hypergeometric test: classes are treated as sets of individual metabolites and all metabolites are treated as equally informative. This function uses Food-Biomarker Ontology knowledge as biological information.

Usage

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ora(
  metaboliteList,
  metaboliteUniverse,
  subOntology = "food",
  pvalCutoff = 0.01,
  fobi = fobitools::fobi
)

Arguments

metaboliteList

A vector of FOBI metabolite identifiers that define the selected list of metabolites.

metaboliteUniverse

A vector of FOBI metabolite identifiers that define the universe of possible metabolites (all metabolites analyzed in the study).

subOntology

A character string specifying one of the two FOBI sub-ontologies: "food", or "biomarker".

pvalCutoff

A numeric value indicating a p-value cutoff for raw p-values generated by hypergeometric test.

fobi

FOBI table obtained with 'parse_fobi()'. If this value is set to NULL, the last version of FOBI will be downloaded from GitHub.

Value

A tibble with ORA results.

Author(s)

Pol Castellano-Escuder

References

G. Korotkevich, V. Sukhov, A. Sergushichev. Fast gene set enrichment analysis. bioRxiv (2019), doi:10.1101/060012

Pol Castellano-Escuder, Raúl González-Domínguez, David S Wishart, Cristina Andrés-Lacueva, Alex Sánchez-Pla, FOBI: an ontology to represent food intake data and associate it with metabolomic data, Database, Volume 2020, 2020, baaa033, https://doi.org/10.1093/databa/baaa033.

Examples

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metaboliteUniverse <- c(fobitools::idmap$FOBI[1:200], fobitools::idmap$FOBI[400:450])
metaboliteList <- c(fobitools::idmap$FOBI[1:50], fobitools::idmap$FOBI[70:80])

# Food enrichment analysis
fobitools::ora(metaboliteList = metaboliteList, 
               metaboliteUniverse = metaboliteUniverse, 
               pvalCutoff = 1)

# Chemical class enrichment analysis
fobitools::ora(metaboliteList = metaboliteList, 
               metaboliteUniverse = metaboliteUniverse, 
               subOntology = "biomarker", 
               pvalCutoff = 1)

pcastellanoescuder/FOBIEnrichR documentation built on Jan. 15, 2022, 8:03 a.m.