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

Assess the contribution of the targeted precursor in fragmentation acquired or anticipated isolation windows using a metric called "precursor purity". Also provides simple processing steps (averaging, filtering, blank subtraction, etc) for DI-MS data. Works for both LC-MS(/MS) and DI-MS(/MS) data.

Author
Thomas N. Lawson, Ralf Weber, Martin Jones, Mark Viant, Warwick Dunn
Date of publication
None
Maintainer
Thomas N. Lawson <thomas.nigel.lawson@gmail.com>
License
GPL (>= 2)
Version
1.0.0

View on Bioconductor

Man pages

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

Files in this package

msPurity/.travis.yml
msPurity/DESCRIPTION
msPurity/NAMESPACE
msPurity/NEWS
msPurity/R
msPurity/R/all-generics.R
msPurity/R/iw-norm.R
msPurity/R/pcalc.R
msPurity/R/purityA-class.R
msPurity/R/purityA-constructor.R
msPurity/R/purityA-frag4feature.R
msPurity/R/purityA-validate.R
msPurity/R/purityD-av-spectra.R
msPurity/R/purityD-class.R
msPurity/R/purityD-constructor.R
msPurity/R/purityD-dims-purity.R
msPurity/R/purityD-fileList.R
msPurity/R/purityD-filterp.R
msPurity/R/purityD-subtract.R
msPurity/R/purityD-writeOut.R
msPurity/R/purityX-class.R
msPurity/R/purityX-constructor.R
msPurity/R/spectral-complexity.R
msPurity/R/splinepurity.R
msPurity/README.md
msPurity/appveyor.yml
msPurity/build
msPurity/build/vignette.rds
msPurity/inst
msPurity/inst/doc
msPurity/inst/doc/msPurity-vignette.R
msPurity/inst/doc/msPurity-vignette.Rmd
msPurity/inst/doc/msPurity-vignette.html
msPurity/inst/extdata
msPurity/inst/extdata/iwqe5.rds
msPurity/man
msPurity/man/Getfiles.Rd
msPurity/man/assessPuritySingle.Rd
msPurity/man/averageSpectra-purityD-method.Rd
msPurity/man/averageSpectraSingle.Rd
msPurity/man/dimsPredictPurity-purityD-method.Rd
msPurity/man/dimsPredictPuritySingle.Rd
msPurity/man/filterp-purityD-method.Rd
msPurity/man/frag4feature-purityA-method.Rd
msPurity/man/getP-purityD-method.Rd
msPurity/man/groupPeaks-purityD-method.Rd
msPurity/man/groupPeaksEx.Rd
msPurity/man/initialize-purityD-method.Rd
msPurity/man/purityA.Rd
msPurity/man/purityD-class.Rd
msPurity/man/purityX.Rd
msPurity/man/show-purityA-method.Rd
msPurity/man/show-purityD-method.Rd
msPurity/man/show-purityX-method.Rd
msPurity/man/subtract-purityD-method.Rd
msPurity/man/subtractMZ.Rd
msPurity/man/validate-purityA-method.Rd
msPurity/man/writeOut-purityD-method.Rd
msPurity/tests
msPurity/tests/testthat
msPurity/tests/testthat.R
msPurity/tests/testthat/test.dims.R
msPurity/tests/testthat/test.lcms.R
msPurity/vignettes
msPurity/vignettes/msPurity-vignette.Rmd
msPurity/vignettes/mspurity.bib