cosmiq

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see cosmiq.

cosmiq - COmbining Single Masses Into Quantities


Bioconductor version: 3.7

cosmiq is a tool for the preprocessing of liquid- or gas - chromatography mass spectrometry (LCMS/GCMS) data with a focus on metabolomics or lipidomics applications. To improve the detection of low abundant signals, cosmiq generates master maps of the mZ/RT space from all acquired runs before a peak detection algorithm is applied. The result is a more robust identification and quantification of low-intensity MS signals compared to conventional approaches where peak picking is performed in each LCMS/GCMS file separately. The cosmiq package builds on the xcmsSet object structure and can be therefore integrated well with the package xcms as an alternative preprocessing step.

Author: David Fischer <dajofischer at googlemail.com>, Christian Panse <cp at fgcz.ethz.ch>, Endre Laczko <endre.laczko at fgcz.uzh.ch>

Maintainer: David Fischer <dajofischer at googlemail.com>, Christian Panse <cp at fgcz.ethz.ch>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("cosmiq")

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("cosmiq")
13th Annual Conference of the Metabolomics Society 2017 poster P-32 PDF R Script
cosmiq primer PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews MassSpectrometry, Metabolomics, Software
Version 1.13.0
In Bioconductor since BioC 3.0 (R-3.1) (9.5 years)
License GPL-3
Depends R (>= 3.0.2), Rcpp
Imports pracma, xcms, MassSpecWavelet, faahKO
System Requirements
URL http://www.bioconductor.org/packages/devel/bioc/html/cosmiq.html
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Suggests RUnit, BiocGenerics, BiocStyle
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Package Archives

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

Source Package cosmiq_1.13.0.tar.gz
Windows Binary cosmiq_1.14.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) cosmiq_1.13.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/cosmiq
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/cosmiq
Package Short Url https://bioconductor.org/packages/cosmiq/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive