ora {fobitools} | R Documentation

## Classical Over Representation Analysis with FOBI

### 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

    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

    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)

[Package fobitools version 1.0.0 Index]