cosmiq: cosmiq - COmbining Single Masses Into Quantities

Share:

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@googlemail.com>, Christian Panse <cp@fgcz.ethz.ch>, Endre Laczko <endre.laczko@fgcz.uzh.ch>
Date of publication
None
Maintainer
David Fischer <dajofischer@googlemail.com>, Christian Panse <cp@fgcz.ethz.ch>
License
GPL-3
Version
1.8.0
URLs

View on Bioconductor

Man pages

combine_spectra
Combine mass spectra of each scan and each file into a single...
cosmiq
cosmiq - main wrapper function
create_datamatrix
Quantifying mz/RT intensities using peak locations from...
eicmatrix
Generate matrix of combined extraced ion chromatograms (EICs)
peakdetection
An algorithm for the detection of peak locations and...
quantify_combined
Generate report with combined ion intensities
retention_time
Detection of chromatographic peak locations from extracted...

Files in this package

cosmiq/DESCRIPTION
cosmiq/NAMESPACE
cosmiq/NEWS
cosmiq/R
cosmiq/R/combine_spectra.R
cosmiq/R/cosmiq.R
cosmiq/R/create_datamatrix.R
cosmiq/R/eicmatrix.R
cosmiq/R/peakdetection.R
cosmiq/R/quantify_combined.R
cosmiq/R/retention_time.R
cosmiq/build
cosmiq/build/vignette.rds
cosmiq/inst
cosmiq/inst/Dockerfile
cosmiq/inst/doc
cosmiq/inst/doc/cosmiq.R
cosmiq/inst/doc/cosmiq.Rnw
cosmiq/inst/doc/cosmiq.pdf
cosmiq/inst/unitTests
cosmiq/inst/unitTests/test_cosmiq.R
cosmiq/man
cosmiq/man/combine_spectra.Rd
cosmiq/man/cosmiq.Rd
cosmiq/man/create_datamatrix.Rd
cosmiq/man/eicmatrix.Rd
cosmiq/man/peakdetection.Rd
cosmiq/man/quantify_combined.Rd
cosmiq/man/retention_time.Rd
cosmiq/src
cosmiq/src/Makevars
cosmiq/src/util.c
cosmiq/tests
cosmiq/tests/runTests.R
cosmiq/vignettes
cosmiq/vignettes/cosmiq.Rnw
cosmiq/vignettes/cosmiq.bib