GetSiriusWidget: GetSiriusWidget

In mjhelf/Metaboseek: Metaboseek platform

GetSiriusWidget

Description

Widget that starts a SIRIUS analysis as specified in reactives(, which will add an entry to the index file in the SIRIUS folder to be observed by the SiriusModule

Usage

GetSiriusWidget(
  input,
  output,
  session,
  reactives = reactive({     list(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) })
)

GetSiriusWidgetUI(id)

Arguments

input	arguments necessary for use with callModule()
output	arguments necessary for use with callModule()
session	arguments necessary for use with callModule()
reactives	a reactive() returning a list of runSirius() parameters
id	id to be used to define a namespace via NS() (must match id in callModule for the server Module)

Functions

• GetSiriusWidget: server logic

• GetSiriusWidgetUI: UI elements

mjhelf/Metaboseek documentation built on April 23, 2022, 12:09 p.m.