Man pages for WMBEdmands/CompMS2miner
an automatable metabolite identification, visualization and data-sharing R package for high-resolution LC-MS datasets

addNoMS2add no MS2 data to compMS2 class object internal to...
adduct2massconverts ESI adduct names into table of monoisotopic masses
annoCompoundClassautomatically annotate compound classes comments table
cfmFragGraphGencfm fragment graph generation from table of annotations
cleanAbsAdapted from PubMedWordCloud (cleanAbstracts) to work with...
combineMS2combineMS2 ions either within and/ or between composite...
combineMS2.IonsCombine spectra peaks within individual spectra
combineMS2.removeContamremove any possible contaminants identified as repeating...
combineMS2.Spectracombine ions across spectra matched to the same MS1 feature
compMS2-classcompMS2-class
compMS2ConstructConstructor for compMS2 class object from a peak table and...
compMS2Createcreate a compMS2 object
compMS2ExplorerVisualize your compMS2Miner results output using a shiny app.
compMS2MinercompMS2Miner: a package to identify/ visualize unknowns in...
couchDBcurateCouchDB login send CompMS2 data set to couchDB
couchDBpingReqCouchDBpingReq send ping to couch db using log in credentials...
deconvNoiseFilter spectral noise from a CompMS2 class object
deconvNoise.DNFSpectral noise filtration using dynamic noise filter
dotProdMatrixdot product matrix calculation
drugBankdrugBank Database
dynamicNoiseFilterDynamic Noise filtration
exactMassEleelemental monoisotopic masses and natural abundances
example_mzXML_MS1featuresexample mzXML files and MS1 feature table (subset to 820 -...
falsePosIdentifyIdentify and/or remove false positives from metID comments...
form2Matmol formula to element count table
formulaFilterfilter potential formulae based on maximum element by mass...
getAbsAdapted from PubMedWordCloud to work with compMS2Miner
getLoginDetailsGet Login details for CouchDB
getTitlesget PubMed title function adapted from PubChemWordcloud...
HMDBHuman Metabolome Database
lipidAbbrevlipid abbreviations table for pubmed text mining
LMSDLipid Maps Structure Database (LMSD)
metFragAdductsdata.frame of customizable metFrag adduct types and codes
metFragClmetFrag command line function for localSDF files
metIDCombinatorial metabolite identification methods
metID.buildConsensusBuild consensus combinatorial metabolite identification
metID.CFMWrapper function for Competitive Fragmentation modelling...
metID.chemSimtanimoto chemical similarity first network neighbours
metID.compMS2toMspmsp file from compMS2 class object
metID.corrNetworkCompMS2 correlation network generation
metID.dbAnnotateAnnotate unknown features in a compMS2 class object to...
metID.dbProbselects best annotations based on substructure annotations...
metID.matchSpectralDBmatch spectra to spectral databases in the .msp file format...
metID.metFragmetFrag _in silico_ fragmentation query wrapper function
metID.optimConsensusdifferential evolution build consensus weight optimization
metID.predSMILESPhase II metabolite prediction
metID.rtPredQuantitative Structure-Retention Relationship modelling...
metID.specSimNetworkCompMS2 spectral similarity network generation
mfSearchPUGSearch pubmed compound for molecular formula using the...
monoMassMatchMonoisotopic mass matching unknown to data base entry
MS1MatchSpectraMS1featureMatch
MS2fileInfoMS2 file information
optimCutOffoptimum cutoff for a correlation or spectral similarity...
PMIDsearchcustomized PMID search function adapted from PubChemWordcloud...
publishAppPublish your compMS2Explorer app on shinyapps.io
pubMedSearchreturn cleaned abstracts from pubmed from searched key words
ReSpectReSpect Database for Phytochemicals
runGitHubApprun github shiny modified from shiny and devtools
signalGroupingSignal grouping
smiles2FormConvert SMILES code to atomic formula
smiles2MonoMassFormConvert SMILES code to monoisotopic mass and formula
subFormulaesubtract atomic formula y from atomic formula x
subsetCompMS2subset compMS2 class object using a vector of spectra names
subStructureIdentify substructures within composite spectra
subStructure.Annotatecomposite spectra substructure annotation
Substructure_massesCollection of mass spectral fragment/ neutral loss/ adduct...
subStructure.probIdentifies probable substructure type
subStructure.probSummarysummarizes most probable substructure type within all...
T3DBT3DB: Toxin and the toxin-target database
trueFalseSumsummary of true positive and false negative assignments for...
WMBEdmands/CompMS2miner documentation built on June 3, 2017, 8:50 a.m.