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.

AuthorThomas N. Lawson, Ralf Weber, Martin Jones, Mark Viant, Warwick Dunn
Date of publicationNone
MaintainerThomas N. Lawson <thomas.nigel.lawson@gmail.com>
LicenseGPL (>= 2)
Version1.0.0

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

Functions

assessPuritySingle Man page
averageSpectra Man page
averageSpectra,purityD-method Man page
averageSpectraSingle Man page
dimsPredictPurity Man page
dimsPredictPurity,purityD-method Man page
dimsPredictPuritySingle Man page
filterp Man page
filterp,purityD-method Man page
frag4feature Man page
frag4feature,purityA-method Man page
Getfiles Man page
getP Man page
getP,purityD-method Man page
groupPeaks Man page
groupPeaksEx Man page
groupPeaks,purityD-method Man page
initialize,purityD-method Man page
purityA Man page
purityD Man page
purityD-class Man page
purityX Man page
show,purityA-method Man page
show,purityD-method Man page
show,purityX-method Man page
subtract Man page
subtractMZ Man page
subtract,purityD-method Man page
validate Man page
validate,purityA-method Man page
writeOut Man page
writeOut,purityD-method Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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