Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics


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Documentation for package ‘msPurity’ version 1.0.0

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assessPuritySingle Assess the purity of a single LC-MS/MS or DI-MS/MS file
averageSpectra Using purityD object, calculates to average mz, intensity and signal-to-noise of multiple scans from multiple MS datafiles (mzML or .csv)
averageSpectra-method Using purityD object, calculates to average mz, intensity and signal-to-noise of multiple scans from multiple MS datafiles (mzML or .csv)
averageSpectraSingle Calculates to average mz, intensity and signal-to-noise of multiple scans from 1 MS datafile (mzML or .csv)
dimsPredictPurity Using purityD object, assess anticipated purity from a DI-MS run
dimsPredictPurity-method Using purityD object, assess anticipated purity from a DI-MS run
dimsPredictPuritySingle Predict the precursor purity from a DI-MS dataset
filterp Filter out peaks based on intensity and RSD criteria
filterp-method Filter out peaks based on intensity and RSD criteria
frag4feature Assign precursor purity scored fragmentation spectra to XCMS features
frag4feature-method Assign precursor purity scored fragmentation spectra to XCMS features
Getfiles Get files for DI-MS processing
getP Get peaklist for a purityD object
getP-method Get peaklist for a purityD object
groupPeaks Using purityD object, group multiple peaklists by similar mz values (mzML or .csv)
groupPeaks-method Using purityD object, group multiple peaklists by similar mz values (mzML or .csv)
groupPeaksEx Group peaklists from a list of dataframes
initialize-method Constructor for S4 class to represent a DI-MS purityD
purityA Assess the purity of multiple LC-MS/MS or DI-MS/MS files (constructor)
purityD An S4 class to represent a DI-MS purityD
purityD-class An S4 class to represent a DI-MS purityD
purityX Assessing anticipated purity of XCMS features from an LC-MS run
show-method Show method for purityA class
show-method Show method for purityD
show-method Show method for purityX
subtract Using Subtract MZ values based on ppm tolerance and noise ratio
subtract-method Using Subtract MZ values based on ppm tolerance and noise ratio
subtractMZ Subtract MZ values based on ppm tolerance and noise ratio
validate Validate precursor purity predictions using LC-MS and LC-MS/MS dataset
validate-method Validate precursor purity predictions using LC-MS and LC-MS/MS dataset
writeOut Using purityD object, save peaks as text files
writeOut-method Using purityD object, save peaks as text files