msPurity: Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics
Version 1.2.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorThomas N. Lawson, Ralf Weber, Martin Jones, Mark Viant, Warwick Dunn
Bioconductor views MassSpectrometry Metabolomics Software
Date of publicationNone
MaintainerThomas N. Lawson <thomas.nigel.lawson@gmail.com>
LicenseGPL (>= 2)
Version1.2.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("msPurity")

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
pcalc: Perform purity calculation on a peak matrix
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

CV Source code
Getfiles Man page Source code
MHmakeRandomString Source code
assessPuritySingle Man page Source code
averageCluster Source code
averageSpectra Man page
averageSpectra,purityD-method Man page
averageSpectraSingle Man page Source code
calculateFWHM Source code
check_ppm Source code
cleanUp Source code
clustering Source code
convert2Raw Source code
covar Source code
dimsPredictPurity Man page
dimsPredictPurity,purityD-method Man page
dimsPredictPuritySingle Man page Source code
dimsPredictPuritySingleMz Source code
filterp Man page
filterp,purityD-method Man page
frag4feature Man page
frag4feature,purityA-method Man page
fsub1 Source code
fsub2 Source code
getEic Source code
getMS2scans Source code
getP Man page
getP,purityD-method Man page
getScanLoop Source code
getTic Source code
get_init_purity Source code
get_interp_purity Source code
get_iso_intensity_range Source code
get_isolation_offsets Source code
get_prec_scans Source code
getmrdf Source code
getname Source code
getscans Source code
group1d Source code
groupPeaks Man page
groupPeaks,purityD-method Man page
groupPeaksEx Man page Source code
grpByXCMS Source code
im_tag Source code
initialize,purityD-method Man page
iwNormGauss Source code
iwNormQE.5 Source code
iwNormRcosine Source code
linearPurity Source code
missing_prec_scan Source code
msfrProcess Source code
mzMLProcess Source code
mzmatching Source code
overlap Source code
pcalc Man page Source code
performHc Source code
plotPurity Source code
pp4file Source code
ppm_diff Source code
predictPurityExp Source code
predictPurityLCMSloop Source code
purityA Man page Source code
purityD Man page
purityD-class Man page
purityX Man page Source code
removeIsotopes Source code
rsde Source code
show,purityA-method Man page
show,purityD-method Man page
show,purityX-method Man page
snrFilter Source code
splinePurity Source code
stde Source code Source code
stderror Source code
subtract Man page
subtract,purityD-method Man page
subtractMZ Man page Source code
subtractSingle Source code
validate Man page
validate,purityA-method Man page
writeOut Man page
writeOut,purityD-method Man page

Files

.travis.yml
DESCRIPTION
NAMESPACE
NEWS
R
R/all-generics.R
R/iw-norm.R
R/pcalc.R
R/purityA-class.R
R/purityA-constructor.R
R/purityA-frag4feature.R
R/purityA-validate.R
R/purityD-av-spectra.R
R/purityD-class.R
R/purityD-constructor.R
R/purityD-dims-purity.R
R/purityD-fileList.R
R/purityD-filterp.R
R/purityD-subtract.R
R/purityD-writeOut.R
R/purityX-class.R
R/purityX-constructor.R
R/spectral-complexity.R
R/splinepurity.R
README.md
appveyor.yml
build
build/vignette.rds
inst
inst/doc
inst/doc/msPurity-vignette.R
inst/doc/msPurity-vignette.Rmd
inst/doc/msPurity-vignette.html
inst/extdata
inst/extdata/iwqe5.rds
man
man/Getfiles.Rd
man/assessPuritySingle.Rd
man/averageSpectra-purityD-method.Rd
man/averageSpectraSingle.Rd
man/dimsPredictPurity-purityD-method.Rd
man/dimsPredictPuritySingle.Rd
man/filterp-purityD-method.Rd
man/frag4feature-purityA-method.Rd
man/getP-purityD-method.Rd
man/groupPeaks-purityD-method.Rd
man/groupPeaksEx.Rd
man/initialize-purityD-method.Rd
man/pcalc.Rd
man/purityA.Rd
man/purityD-class.Rd
man/purityX.Rd
man/show-purityA-method.Rd
man/show-purityD-method.Rd
man/show-purityX-method.Rd
man/subtract-purityD-method.Rd
man/subtractMZ.Rd
man/validate-purityA-method.Rd
man/writeOut-purityD-method.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/test.dims.R
tests/testthat/test.lcms.R
tests/testthat/test.pcalc.R
vignettes
vignettes/msPurity-vignette.Rmd
vignettes/mspurity.bib
msPurity documentation built on May 20, 2017, 10:19 p.m.