runSirius: runSirius

In mjhelf/Mosaic: Metaboseek platform

runSirius

Description

run SIRIUS externally for a list of ms2 spectra

Usage

runSirius(
  sirpath = file.path(.MseekOptions$siriusFolder, "sirius"),
  ms2,
  parentmz,
  outfolder = getwd(),
  ms1 = NULL,
  ion = "[M+?]+",
  comments = "",
  rt = "",
  charge = 1,
  fingerid = T,
  scanindices = "",
  moreOpts = "",
  config = list(IsotopeSettings.filter = TRUE, FormulaSearchDB = c("ALL_BUT_INSILICO",
    "ALL", "BIO", "METACYC", "CHEBI", "COCONUT", "ECOCYCMINE", "GNPS", "HMDB", "HSDB",
    "KEGG", "KEGGMINE", "KNAPSACK", "MACONDA", "MESH", "NORMAN", "UNDP", "PLANTCYC",
    "PUBCHEM", "PUBMED", "YMDB", "YMDBMINE", "ZINCBIO"), Timeout.secondsPerTree = 0,
    FormulaSettings.enforced = "HCNOP[5]S", Timeout.secondsPerInstance = 0,
    AdductSettings.detectable =
    "[[M+K]+,[M+H3N+H]+,[M+Na]+,[M-H4O2+H]+,[M-H2O+H]+,[M+H]+]",
    UseHeuristic.mzToUseHeuristicOnly = 650,      AlgorithmProfile = "orbitrap",
    IsotopeMs2Settings = "IGNORE", MS2MassDeviation.allowedMassDeviation = "5.0ppm",
    NumberOfCandidatesPerIon = 1, UseHeuristic.mzToUseHeuristic = 300,
    FormulaSettings.detectable = ",", NumberOfCandidates = 10, StructureSearchDB =
    c("ALL_BUT_INSILICO", "ALL", "BIO", "METACYC", "CHEBI", "COCONUT", "ECOCYCMINE",
    "GNPS", "HMDB", "HSDB", "KEGG", "KEGGMINE", "KNAPSACK", "MACONDA", "MESH", "NORMAN",
    "UNDP", "PLANTCYC", "PUBCHEM", "PUBMED", "YMDB", "YMDBMINE", "ZINCBIO"),     
    AdductSettings.fallback = "[[M+K]+,[M+Na]+,[M+H]+]", RecomputeResults = TRUE),
  force = T
)

Arguments

sirpath	path to SIRIUS executable
ms2	a list (or list of lists) of ms2 spectra (matrices with columns mz and intensity), see Details
parentmz	numeric: parent ion m/z value
outfolder	output folder for the SIRIUS results
ms1	if not NULL, a list of MS1 spectra
ion	ion type (e.g. [M+H]+)
comments	character: comments
rt	numeric: retention time in seconds
charge	charge (positive or negative integer)
fingerid	if TRUE, will try to predict structures with CSI:FingerID
scanindices	which scans were averaged into this ms2 spectrum
moreOpts	character with additional options to be passed to SIRIUS
config	list containing sirius configuration
force	force calculation, even if same results should exist according to indexfile

Details

ms2

can be a list of matrices, or a list of list of matrices. In the latter case, the (optional) names of the nested list items are expected to be in the format "collisionXX", where XX denotes an integer collision energy.

Value

Will cause SIRIUS to run a job and save its results in a timestamped subfolder of outfolder, and will register the job in the index.csv file in outfolder.

mjhelf/Mosaic documentation built on April 28, 2022, 11:32 a.m.