msPurity

DOI: 10.18129/B9.bioc.msPurity    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see msPurity.

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

Bioconductor version: 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>

Installation

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

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

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	ImmunoOncology, MassSpectrometry, Metabolomics, Software
Version	1.8.1
In Bioconductor since	BioC 3.4 (R-3.3) (2.5 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_1.8.1.tar.gz
Windows Binary	msPurity_1.8.1.zip
Mac OS X 10.11 (El Capitan)	msPurity_1.8.1.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