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 <email@example.com>, Christian Panse <firstname.lastname@example.org>, Endre Laczko <email@example.com>|
|Bioconductor views||MassSpectrometry Metabolomics|
|Date of publication||None|
|Maintainer||David Fischer <firstname.lastname@example.org>, Christian Panse <email@example.com>|
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...
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