msPurity

DOI: 10.18129/B9.bioc.msPurity    

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

Bioconductor version: Release (3.8)

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. Spectral matching of fragmentation spectra can also be run against a SQLite database of library spectra.

Author: Thomas N. Lawson, Ralf Weber, Martin Jones, Mark Viant, Warwick Dunn

Maintainer: Thomas N. Lawson <thomas.nigel.lawson at gmail.com>

Citation (from within R, enter citation("msPurity")):

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("msPurity", version = "3.8")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("msPurity")

 

HTML R Script msPurity
HTML R Script msPurity spectral matching
PDF   Reference Manual
Text   NEWS

Details

biocViews MassSpectrometry, Metabolomics, Software
Version 1.8.0
In Bioconductor since BioC 3.4 (R-3.3) (2 years)
License GPL (>= 2)
Depends Rcpp
Imports plyr, foreach, parallel, doSNOW, stringr, mzR, reshape2, fastcluster, ggplot2, DBI, RSQLite
LinkingTo
Suggests testthat, xcms, BiocStyle, knitr, rmarkdown, msPurityData, CAMERA
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package msPurity_1.8.0.tar.gz
Windows Binary msPurity_1.8.0.zip
Mac OS X 10.11 (El Capitan) msPurity_1.8.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/msPurity
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/msPurity
Package Short Url http://bioconductor.org/packages/msPurity/
Package Downloads Report Download Stats

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