Load enrichment background

Load_background() retrieves a list of terms and associated metabolites for enrichment based on requested molecule type, background type and input feature type.

Usage

Load_background(
  mol_type = c("Lipid", "Metabo"),
  bg_type = c("LION", "main_class", "super_class", "sub_class", "pathway"),
  feature_type = c("sf", "name")
)

Arguments

mol_type

Character indicating molecule type. Can be either Lipid for Lipids and Metabo for small molecules

bg_type

Character indicating background type :

"LION"

LION ontology for lipids only.

"main_class"

Level 1 classification - finer classification compared to super_class.

"super_class"

Level 0 classification.

"sub_class"

Level 2 classification - finer classification compared to main_class.

"pathways"

Biological pathways based on KEGG, Reactome, and SMPDB.

feature_type

Character indicating input feature type. Can be either sf for sum formula or ion and name for molecule name.

Value

List where each element name correspond to a given term and values are either metabolite names or sum formulas.

Examples

if (FALSE) { # \dontrun{
bg <-
Load_background(mol_type = "Metabo",
                   bg_type = "main_class",
                   feature_type = "name")
} # }