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DESCRIPTION
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DESCRIPTION
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Package: msPurity
Type: Package
Title: Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based
Fragmentation in Metabolomics
Version: 1.13.0
Date: 2019-10-04
Author: Thomas N. Lawson, Ralf Weber, Martin Jones, Mark Viant, Warwick Dunn
Maintainer: Thomas N. Lawson <[email protected]>
Description: msPurity R package was developed to:
1) Assess the spectral quality of fragmentation spectra by evaluating the "precursor ion purity".
2) Process fragmentation spectra.
3) Perform spectral matching.
What is precursor ion purity? -What we call "Precursor ion purity" is a measure of the
contribution of a selected precursor peak in an isolation window used for fragmentation.
The simple calculation involves dividing the intensity of the selected precursor peak by the
total intensity of the isolation window. When assessing MS/MS spectra this calculation is
done before and after the MS/MS scan of interest and the purity is interpolated at the
recorded time of the MS/MS acquisition. Additionally, isotopic peaks can be removed,
low abundance peaks are removed that are thought to have limited contribution to the
resulting MS/MS spectra and the isolation efficiency of the mass spectrometer can be used
to normalise the intensities used for the calculation.
Encoding: UTF-8
License: GPL (>= 2)
LazyData: TRUE
BugReports: https://github.com/computational-metabolomics/msPurity/issues/new
Depends:
Rcpp
Imports:
plyr,
dplyr,
dbplyr,
magrittr,
foreach,
parallel,
doSNOW,
stringr,
mzR,
reshape2,
fastcluster,
ggplot2,
DBI,
RSQLite,
uuid,
jsonlite
Suggests:
testthat,
xcms,
BiocStyle,
knitr,
rmarkdown,
msPurityData,
CAMERA,
RPostgres,
RMySQL
VignetteBuilder: knitr
RoxygenNote: 6.1.1
biocViews: MassSpectrometry, Metabolomics, Software
Collate:
'all-generics.R'
'averaging.R'
'combineAnnotations.R'
'create-database.R'
'createDatabase.R'
'flag-filter-remove.R'
'iw-norm.R'
'matching-algs.R'
'meta_extract.R'
'msPurity.R'
'pcalc.R'
'purityA-0-class.R'
'purityA-av-spectra.R'
'purityA-constructor.R'
'purityA-create-msp.R'
'purityA-filter-frag-spectra.R'
'purityA-frag4feature.R'
'purityA-validate.R'
'purityD-class.R'
'purityD-constructor.R'
'purityD-av-spectra.R'
'purityD-dims-purity.R'
'purityD-fileList.R'
'purityD-filterp.R'
'purityD-subtract.R'
'purityD-writeOut.R'
'purityX-class.R'
'purityX-constructor.R'
'spectral-matching.R'
'spectralMatching.R'
'splinepurity.R'