Files in michaelwitting/masstrixR
Annotation of MS based metabolomics data

.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/MS1_AdductDbCreate.R R/MS1_AdductDbSearch.R R/MS1_IsotopePattern.R R/MS1_Utilities.R R/MS1_isotopePattern.R R/MS2_LibraryReader.R R/MS2_SpectrumDbCreate.R R/MS2_SpectrumDbSearch.R R/MS2_Utilities.R R/MS2_specSimilarty.R R/Utils_ParseAgilent.R R/Utils_ParseGenedata.R R/Utils_SpectraImportExport.R R/Utils_TidyFunctions.R R/Utils_plotting.R R/Utils_spectrumFunctions.R README.md
data/isotopes.rda
inst/extdata/databases/chebi_20190125.txt
inst/extdata/databases/hmdb_20190125.txt
inst/extdata/databases/lipidMaps_20190125.txt
inst/extdata/databases/wormJam_20190613.txt
inst/extdata/databases/ymdb_20190125.txt
inst/extdata/exampleData/Celegans_lipids_ms2/ceramides.mgf
inst/extdata/exampleData/Celegans_lipids_ms2/wormLipidDb_MS2.sqlite
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000101.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000201.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000202.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000301.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000302.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000303.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000401.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000402.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000403.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000501.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000502.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000503.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000601.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000602.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000603.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000701.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000702.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000703.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000801.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000802.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000803.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000901.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000902.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000903.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP001001.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP001002.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP001003.txt
inst/extdata/exampleData/Celegans_ms2/exampleMs2.mgf
inst/extdata/exampleData/Celegans_mz/NaAcHILICPos_Cluster.gda
inst/extdata/exampleData/Celegans_mz_rt/peakTable.txt
inst/extdata/exampleData/Celegans_mz_rt/rtidb.txt
inst/extdata/exampleData/databases/example_pos_MH_MNa.sqlite
inst/extdata/exampleData/databases/ymdb_example.txt
inst/extdata/exampleData/listFormats/Agilent_CEF.cef
inst/scripts/massBankRecords.R inst/scripts/metfragR.R inst/scripts/readGenedataPmt.R man/alignSpectra.Rd man/bin_Spectra.Rd man/bin_Spectrum.Rd man/calcAdductFormula.Rd man/calculateExactMass.Rd man/calculateKendrickMass.Rd man/calculateKendrickMassDefect.Rd man/calculateNominalKendrickMass.Rd man/calculateRefKendrickMassDefect.Rd man/checkRmkd.Rd man/cleanSpectra.Rd man/commonPeaks.Rd man/containsFormula.Rd man/containsFragmentDifference.Rd man/containsNeutralLossIon.Rd man/containsProductIon.Rd man/createDb.Rd man/createMs2Db.Rd man/createResultsSet.Rd man/dot-bin_values.Rd man/dot-fix_breaks.Rd man/dot-kegg.Rd man/dotproduct.Rd man/filterIsotopePeaks.Rd man/forwardDotProduct.Rd man/generateChemFormula.Rd man/getAdductCalc.Rd man/getAdductNames.Rd man/getAllNegModeAdducts.Rd man/getAllPosModeAdducts.Rd man/getExternalDbIds.Rd man/getIsotopeAddList.Rd man/getNeutralLossCalc.Rd man/ionFormulaSearch.Rd man/isoPatternSimilarity.Rd man/massShiftForwadDotProduct.Rd man/matchMassDiff.Rd man/match_mz_inter.Rd man/match_mz_intra.Rd man/mzSearch.Rd man/neutralFormulaSearch.Rd man/parseChemFormula.Rd man/predictIsoPattern.Rd man/prepareCompoundList.Rd man/prepareIsoCompoundList.Rd man/readAnnotatedMgfData.Rd man/readGdaFile.Rd man/readMassBankFile.Rd man/readMassBankFolder.Rd man/reconstructIsoPattern.Rd man/reverseDotProduct.Rd man/scoreIsoPattern.Rd man/searchByExactMassOnline.Rd man/searchByFormulaOnline.Rd man/searchByPrecursor.Rd man/searchByPrecursorOnline.Rd man/standardizeChemFormula.Rd man/validateCompoundList.Rd man/xRank.Rd
masstrixR.Rproj
tests/testthat/test_ion_matching.R
vignettes/example_MS2.sqlite
vignettes/example_isoLabel_pos_MH_MNa.sqlite
vignettes/example_pos_MH_MNa.sqlite
vignettes/example_pos_MH_MNa_withRT.sqlite
vignettes/masstrixR_createSQLiteDB_MS1.Rmd vignettes/masstrixR_createSQLiteDB_MS2.Rmd vignettes/masstrixR_ms2Functions.Rmd vignettes/masstrixR_ms2Matching.Rmd vignettes/masstrixR_mzCcsMatching.Rmd vignettes/masstrixR_mzMatching.Rmd vignettes/masstrixR_mzRtMatching.Rmd
michaelwitting/masstrixR documentation built on Aug. 18, 2019, 1:33 a.m.