msea: Performs a preranked metabolite set enrichment analysis...

In pcastellanoescuder/fobitools: Tools for Manipulating the FOBI Ontology

Performs a preranked metabolite set enrichment analysis (MSEA)

Description

This function performs a MSEA based on the adaptive multilevel splitting Monte Carlo approach.

Usage

msea(
  metaboliteRanks,
  subOntology = "food",
  pvalCutoff = 0.01,
  fobi = fobitools::fobi
)

Arguments

metaboliteRanks	A named vector of FOBI metabolite identifiers with their metabolite-level stats.
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 MSEA.
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 MSEA 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

metabolites <- c(fobitools::idmap$FOBI[1:49], fobitools::idmap$FOBI[70:80])
random_pvals <- c(runif(n = length(metabolites)*0.3, min = 0.001, max = 0.05), runif(n = length(metabolites)*0.7, min = 0.05, max = 0.99))
names(random_pvals) <- metabolites
metaboliteRanks <- random_pvals[order(random_pvals)]

# Food enrichment analysis
fobitools::msea(metaboliteRanks = metaboliteRanks, 
                pvalCutoff = 1)

# Chemical class enrichment analysis
fobitools::msea(metaboliteRanks = metaboliteRanks, 
                subOntology = "biomarker", 
                pvalCutoff = 1)

pcastellanoescuder/fobitools documentation built on Dec. 2, 2024, 3:40 a.m.