To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("mzR")

In most cases, you don't need to download the package archive at all.

mzR

 

   

This is the development version of mzR; for the stable release version, see mzR.

parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass spectrometry data)

Bioconductor version: Development (3.4)

mzR provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a wrapper for the ISB random access parser for mass spectrometry mzXML, mzData and mzML files. The package contains the original code written by the ISB, and a subset of the proteowizard library for mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.

Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou

Maintainer: Bernd Fischer <b.fischer at dkfz.de>, Steffen Neumann <sneumann at ipb-halle.de>, Laurent Gatto <lg390 at cam.ac.uk>, Qiang Kou <qkou at umail.iu.edu>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("mzR")

Documentation

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

browseVignettes("mzR")

 

PDF R Script Accessin raw mass spectrometry and identification data
PDF   Reference Manual

Details

biocViews DataImport, Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software
Version 2.7.3
In Bioconductor since BioC 2.9 (R-2.14) (5 years)
License Artistic-2.0
Depends Rcpp (>= 0.10.1), methods, utils
Imports Biobase, BiocGenerics(>= 0.13.6), ProtGenerics
LinkingTo Rcpp, zlibbioc
Suggests msdata(>= 0.3.5), RUnit, mzID, BiocStyle, knitr
SystemRequirements C++11, GNU make, NetCDF
Enhances
URL https://github.com/sneumann/mzR/
BugReports https://github.com/sneumann/mzR/issues/
Depends On Me MSGFgui, MSnbase, xcms
Imports Me MSnID, msPurity, Pbase, ProteomicsAnnotationHubData, RMassBank, SIMAT
Suggests Me AnnotationHub, msdata, qcmetrics, RforProteomics
Build Report  

Package Archives

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

Package Source mzR_2.7.3.tar.gz
Windows Binary mzR_2.7.3.zip (32- & 64-bit)
Mac OS X 10.9 (Mavericks) mzR_2.7.3.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/mzR
Package Short Url http://bioconductor.org/packages/mzR/
Package Downloads Report Download Stats

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