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Configuration fr re-ranking of Molecular Formula Annotation

Source: R/run-param.R
zodiacParam.Rd

This function configures the parameters for the re-ranking of the previously computed molecular formula annotation in Sirius. This step is quite computationally and memory demanding, it is advised to perform it only if de novo structure annotation is used later on

ZODIAC uses the top X molecular formula candidates for each molecule from SIRIUS to build a similarity network, and uses Bayesian statistics to re-rank those candidates.

Usage

zodiacParam(
  consideredCandidatesAt300Mz = 10,
  consideredCandidatesAt800Mz = 50,
  runInTwoSteps = TRUE,
  edgeFilterThreshold = TRUE,
  thresholdFilter = 0.95,
  minLocalCandidates = 1,
  minLocalConnections = 10,
  gibbsSamplerParameters = TRUE,
  iterations = 20000,
  burnInPeriod = 2000,
  numberOfMarkovChains = 10
)

Arguments

consideredCandidatesAt300Mz

An integer(1) specifying the maximum number of candidate molecular formulas considered by ZODIAC for compounds below 300 m/z. Default is 10.

consideredCandidatesAt800Mz

An integer(1) specifying the maximum number of candidate molecular formulas considered by ZODIAC for \ compounds above 800 m/z. Default is 50.

runInTwoSteps

logical specifying whether ZODIAC uses a 2-step approach. First running 'good quality compounds' only, and afterwards including the remaining compounds. Default is TRUE.

edgeFilterThreshold

logical value specifying whether ZODIAC uses an edge filter threshold. Default is TRUE.

thresholdFilter

numeric(1) value specifying the threshold filter. Default is 0.95.

minLocalCandidates

numeric(1) value specifying the minimum number of local candidates. Default is 1.

minLocalConnections

numeric(1) value specifying the minimum number of local connections. Default is 10.

gibbsSamplerParameters

logical value specifying whether ZODIAC uses Gibbs sampler parameters. Default is TRUE.

iterations

numeric(1) specifying the number of iterations. Default is 20000.

burnInPeriod

numeric(1) specifying the burn-in period. Default is 2000.

numberOfMarkovChains

numeric(1) specifying the number of Markov chains. Default is 10.

Value

An object of class zodiacParam.

Note

For more information, see the Sirius documentation.

References

reference

Examples

# Example of setting up the parameter for Zodiac re-ranking
param <- zodiacParam(consideredCandidatesAt300Mz = 10,
                     consideredCandidatesAt800Mz = 50,
                     runInTwoSteps = TRUE,
                     edgeFilterThreshold = TRUE,
                     thresholdFilter = 0.95,
                     minLocalCandidates = 1,
                     minLocalConnections = 10,
                     gibbsSamplerParameters = TRUE,
                     iterations = 20000,
                     burnInPeriod = 2000,
                     numberOfMarkovChains = 10)