msPurity

This package is for version 3.7 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: 3.7

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 (!require("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")

msPurity HTML R Script

msPurity spectral matching HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews MassSpectrometry, Metabolomics, Software

Version 1.6.2

In Bioconductor since BioC 3.4 (R-3.3) (7.5 years)

License GPL (>= 2)

Depends Rcpp

Imports plyr, foreach, parallel, doSNOW, stringr, mzR, reshape2, fastcluster, ggplot2, DBI, RSQLite

System Requirements

URL

Suggests testthat, xcms, BiocStyle, knitr, rmarkdown, msPurityData, CAMERA

Linking To

Enhances

Depends On Me

Imports Me

Suggests Me

Links To Me

Build Report Build Report

Package Archives

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

Source Package msPurity_1.6.2.tar.gz

Windows Binary msPurity_1.6.2.zip

Mac OS X 10.11 (El Capitan) msPurity_1.6.2.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 https://bioconductor.org/packages/msPurity/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.7 Source Archive