Man pages for WMBEdmands/compMS2Miner
an automatable metabolite identification, visualization and data-sharing R package for high-resolution LC-MS datasets
| addNoMS2 | add no MS2 data to compMS2 class object internal to... |
| adduct2mass | converts ESI adduct names into table of monoisotopic masses |
| annoCompoundClass | automatically annotate compound classes comments table |
| cfmFragGraphGen | cfm fragment graph generation from table of annotations |
| cleanAbs | Adapted from PubMedWordCloud (cleanAbstracts) to work with... |
| combineMS2 | combineMS2 ions either within and/ or between composite... |
| combineMS2.Ions | Combine spectra peaks within individual spectra |
| combineMS2.removeContam | remove any possible contaminants identified as repeating... |
| combineMS2.Spectra | combine ions across spectra matched to the same MS1 feature |
| compMS2-class | compMS2-class |
| compMS2Construct | Constructor for compMS2 class object from a peak table and... |
| compMS2Create | create a compMS2 object |
| compMS2Explorer | Visualize your compMS2Miner results output using a shiny app. |
| compMS2Miner | compMS2Miner: a package to identify/ visualize unknowns in... |
| couchDBcurate | CouchDB login send CompMS2 data set to couchDB |
| couchDBpingReq | CouchDBpingReq send ping to couch db using log in credentials... |
| deconvNoise | Filter spectral noise from a CompMS2 class object |
| deconvNoise.DNF | Spectral noise filtration using dynamic noise filter |
| dotProdMatrix | dot product matrix calculation |
| drugBank | drugBank Database |
| dynamicNoiseFilter | Dynamic Noise filtration |
| exactMassEle | elemental monoisotopic masses and natural abundances |
| example_mzXML_MS1features | example mzXML files and MS1 feature table (subset to 820 -... |
| falsePosIdentify | Identify and/or remove false positives from metID comments... |
| form2Mat | mol formula to element count table |
| formulaFilter | filter potential formulae based on maximum element by mass... |
| getAbs | Adapted from PubMedWordCloud to work with compMS2Miner |
| getLoginDetails | Get Login details for CouchDB |
| getTitles | get PubMed title function adapted from PubChemWordcloud... |
| HMDB | Human Metabolome Database |
| lipidAbbrev | lipid abbreviations table for pubmed text mining |
| LMSD | Lipid Maps Structure Database (LMSD) |
| metFragAdducts | data.frame of customizable metFrag adduct types and codes |
| metFragCl | metFrag command line function for localSDF files |
| metID | Combinatorial metabolite identification methods |
| metID.buildConsensus | Build consensus combinatorial metabolite identification |
| metID.CFM | Wrapper function for Competitive Fragmentation modelling... |
| metID.chemSim | tanimoto chemical similarity first network neighbours |
| metID.compMS2toMsp | msp file from compMS2 class object |
| metID.corrNetwork | CompMS2 correlation network generation |
| metID.dbAnnotate | Annotate unknown features in a compMS2 class object to... |
| metID.dbProb | selects best annotations based on substructure annotations... |
| metID.matchSpectralDB | match spectra to spectral databases in the .msp file format... |
| metID.metFrag | metFrag _in silico_ fragmentation query wrapper function |
| metID.optimConsensus | differential evolution build consensus weight optimization |
| metID.predSMILES | Phase II metabolite prediction |
| metID.rtPred | Quantitative Structure-Retention Relationship modelling... |
| metID.specSimNetwork | CompMS2 spectral similarity network generation |
| mfSearchPUG | Search pubmed compound for molecular formula using the... |
| monoMassMatch | Monoisotopic mass matching unknown to data base entry |
| MS1MatchSpectra | MS1featureMatch |
| MS2fileInfo | MS2 file information |
| optimCutOff | optimum cutoff for a correlation or spectral similarity... |
| PMIDsearch | customized PMID search function adapted from PubChemWordcloud... |
| publishApp | Publish your compMS2Explorer app on shinyapps.io |
| pubMedSearch | return cleaned abstracts from pubmed from searched key words |
| ReSpect | ReSpect Database for Phytochemicals |
| runGitHubApp | run github shiny modified from shiny and devtools |
| signalGrouping | Signal grouping |
| smiles2Form | Convert SMILES code to atomic formula |
| smiles2MonoMassForm | Convert SMILES code to monoisotopic mass and formula |
| subFormulae | subtract atomic formula y from atomic formula x |
| subsetCompMS2 | subset compMS2 class object using a vector of spectra names |
| subStructure | Identify substructures within composite spectra |
| subStructure.Annotate | composite spectra substructure annotation |
| Substructure_masses | Collection of mass spectral fragment/ neutral loss/ adduct... |
| subStructure.prob | Identifies probable substructure type |
| subStructure.probSummary | summarizes most probable substructure type within all... |
| T3DB | T3DB: Toxin and the toxin-target database |
| trueFalseSum | summary of true positive and false negative assignments for... |
