Fetch Results from Sirius — results • RuSirius

Functions to retrieve results from the Sirius project, allowing customization of the result type, feature selection, and return format.

Get best match results for a Sirius project. Choose which type of results to fetch with the result.type parameter. "structure" and "deNovo" will both also give information on the formula.

Usage

summary(
  sirius,
  result.type = c("formulaId", "structure", "deNovo", "spectralDbMatch")
)

results(
  sirius,
  features = character(),
  result.type = c("formulaId", "structureDb", "compoundClass", "deNovo",
    "spectralDbMatch", "fragTree"),
  return.type = c("list", "data.frame"),
  topFormula = 5,
  topStructure = 5,
  topSpectralMatches = 5
)

Arguments

sirius: A Sirius object.
result.type: character(1) specifying the type of results to fetch. Options are "formulaId", "structureDb", "compoundClass", "deNovo", "spectralDbMatch", and "fragTree". Defaults to "formulaId".
features: character() vector specifying feature IDs to retrieve results for. Defaults to all available features.
return.type: character(1) specifying return format. Either "data.frame" (default) or "list".
topFormula: numeric(1) Maximum number of formula candidates to retrieve per feature. Defaults to 5.
topStructure: numeric(1) Maximum number of structure candidates per formula. Defaults to 5.
topSpectralMatches: numeric(1) Maximum number of spectral matches per feature. Defaults to 5.

Value

A data.frame or list of results, depending on return.type.

a data.frame with the summary of the results. Important column is the ApproximateConfidence column, which give a score of how possible all the identifications for this feature are. The exactConfidence column is a score of how possible the top identification is.