runSirius: runSirius

View source: R/Functions_SIRIUS.R

runSiriusR Documentation

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.