Structure Database Search — structureDbSearchParam • RuSirius

This function creates an object of class structureDbSearchParam that can be used to configure the structure database search in Sirius. The object can be passed to the runSirius function to perform the structure database search.

By default, SIRIUS searches for molecular structures in a biomolecule structure database. It can also search in the (extremely large) PubChem database or in custom “suspect databases” provided by the user.

Usage

structureDbSearchParam(
  structureSearchDbs = c("BIO", "massbank"),
  tagStructuresWithLipidClass = TRUE,
  expansiveSearchConfidenceMode = c("APPROXIMATE", "EXACT", "OFF")
)

Arguments

structureSearchDbs: character vector, specifying the id of the databases to search for structures. Default is c("BIO", "massbank"). If expansive search is enabled this database selection will be expanded to PubChem if not high confidence hit was found in the selected databases. The available databases can be found by running listDatabases().
tagStructuresWithLipidClass: logical, specifying whether to tag structures with lipid class estimated by El Gordo. The lipid class will only be available if El Gordo predicts that the MS/MS is a lipid spectrum. If this parameter is set to FALSE El Gordo will still be executed and e.g. improve the fragmentation tree, but the matching structure candidates will not be tagged if they match lipid class.
expansiveSearchConfidenceMode: character(1) , specifying the confidence mode for expansive search. Possible values are "APPROXIMATE","EXACT", "OFF". Defaults to "APPROXIMATE".

Value

An object of class structureDbSearchParam.

Note

For more information, see the Sirius documentation.

References

reference

Examples

# Example of setting up the parameters for structure database search
param <- structureDbSearchParam(
                 structureSearchDbs = c("BIO", "massbank"),
                 tagStructuresWithLipidClass = TRUE,
                 expansiveSearchConfidenceMode = "APPROXIMATE")