Data management and analysis of ion trees from ion-trap mass spectrometry


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Documentation for package ‘iontree’ version 1.2.0

Help Pages

iontree-package MSn-iontree: Ion tree management and analysis
buildIonTree Build ion tree
createDB Create a SQLite database
distMS2 Distance metric for MS2 spectral similarity measurement
formatSpec Format mass spec matrix data into a string format, or vice versa
getMetaInfo Get metadata information from data file in mzXML
getMSnRaw Get MSn raw data
hasMS2 Check which samples have MS2 spectra generated
iontree MSn-iontree: Ion tree management and analysis
iontree-class Class "iontree"
metaDataImport Data entry of meta information
mzImport Data entry of iontree into mz table
plot-method Class "iontree"
plot-methods Plot iontree
plotSpectrum Plot a spectrum
rs2iontree Convert a data frame into iontree
saveMSnRaw Retrieve MS2 and MS3 data and save as R binary in the current folder
searchMS2 Search MS2 spectrum from sqlite database
show-method Class "iontree"
show-methods Show methods for class iontree
topIons Retain spectrum with the most intense ions