This function performs a simple over-representation analysis (ORA) on a given list of metabolites and background.
Usage
Run_simple_ORA(
marker_list,
background,
custom_universe = NULL,
alpha_cutoff = 0.05,
min_intersection = 3
)Arguments
- marker_list
A vector or list of marker sets to analyze.
- background
A list of named terms where each term is a character vector of metabolites.
- custom_universe
An optional vector specifying a custom universe of terms. If not provided all metabolites in background will be used as universe.
- alpha_cutoff
A numeric value indicating the alpha cutoff for significance.
- min_intersection
An integer specifying the minimum intersection required between input list and a given term in background.
References
Badia-i-Mompel, P., Nagai, J. S., & Saez-Rodriguez, J. (2022). decoupleR: A flexible tool to handle various modes of biological network analysis. Bioinformatics Advances, 2(1), vbac016. https://doi.org/10.1093/bioadv/vbac016
Examples
if (FALSE) { # \dontrun{
data("example_ORA_markers", package = "S2IsoMErData")
bg = Load_background(mol_type = "Metabo",bg_type = "main_class",feature_type = "sf")
enrich_res = Run_simple_ORA(marker_list = example_ORA_markers,background = bg)
} # }