assessPuritySingle |
Assess the purity of a single LC-MS/MS or DI-MS/MS file |
averageAllFragSpectra |
Using a purityA object, average and filter MS/MS spectra for each XCMS feature within and across MS data files (ignoring intra and inter relationships) |
averageAllFragSpectra-method |
Using a purityA object, average and filter MS/MS spectra for each XCMS feature within and across MS data files (ignoring intra and inter relationships) |
averageInterFragSpectra |
Using a purityA object, average and filter fragmentation spectra for each XCMS feature across multiple MS data files |
averageInterFragSpectra-method |
Using a purityA object, average and filter fragmentation spectra for each XCMS feature across multiple MS data files |
averageIntraFragSpectra |
Using a purityA object, average and filter fragmentation spectra for each XCMS feature within a MS data file |
averageIntraFragSpectra-method |
Using a purityA object, average and filter fragmentation spectra for each XCMS feature within a MS data 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) |
combineAnnotations |
Combine Annotations |
createDatabase |
Create database |
createMSP |
Using a purityA object, create an MSP file of fragmentation spectra |
createMSP-method |
Using a purityA object, create an MSP file of fragmentation spectra |
create_database |
Create database [deprecated] |
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 |
filterFragSpectra |
Filter fragmentations spectra associated with an XCMS feature |
filterFragSpectra-method |
Filter fragmentations spectra associated with an XCMS feature |
filterp |
Filter out peaks based on intensity and RSD criteria |
filterp-method |
Filter out peaks based on intensity and RSD criteria |
flag_remove |
Flag and remove unwanted peaks |
frag4feature |
Using a purityA object, link MS/MS data to XCMS features |
frag4feature-method |
Using a purityA object, link MS/MS data 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 |
get_additional_mzml_meta |
Get additional mzML meta |
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 |
iwNormGauss |
Gaussian normalisation for isolation window efficiency |
iwNormQE.5 |
Q-Exactive +/- 0.5 range, normalisation for isolation window efficiency |
iwNormRcosine |
Raised cosine normalisation for isolation window efficiency |
pcalc |
Perform purity calculation on a peak matrix |
purityA |
Assess the acquired precursor ion purity of MS/MS spectra (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 |
spectralMatching |
Spectral matching for LC-MS/MS datasets |
spectral_matching |
Spectral matching [deprecated] |
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 |