PeakML.Isotope.getChromData: PeakML.Isotope.getChromData

In andzajan/mzmatch.R: mzmatch and PeakML integration for XCMS.

Description

Generates a list of lists containing mass, intensities and retentiontimes of all the isotopes in the isotopeList.

Usage

	PeakML.Isotope.getChromData(isotopeList, chromDataList, phenoData, sampleGroups)

Arguments

isotopeList	List of isotopes see PeakML.Isotope.getIsotopes.
chromDataList	The chrom data list see PeakML.Methods.getChromData.
phenoData	See PeakML.Methods.getPhenoData.
sampleGroups	The sample groups.

Details

The PeakML file format defines an open and extensible file format for storing extracted hyphenated mass spectrometry data. As such, the format will enable users to store intermediate data in a structured manner, but more importantly, to exchange data between different data analysis software. This will give complete flexible control to the users of data analysis software to cherry pick those components best suited to their needs. The PeakML.Methods contains a set of R functions that will enable end users to rapidly write scripts to manipulate PeakML files.

Value

PeakML.Isotope.getChromData returns a list of lists containing mass, intensities and retentiontimes of all the isotopes in the isotopeList. Each sublist will be of the form rtList[[peakGroup]][[sampleGroup]][[isotop]][[replicate]] where the signals/values will be stored.

Author(s)

Achuthanuni Chokkathukalam ([e-mail]) Andris Jankevics ([e-mail])

References

PeakML/mzMatch: A File Format, Java Library, R Library, and Tool-Chain for Mass Spectrometry Data Analysis, Richard A. Scheltema, Andris Jankevics, Ritsert C. Jansen, Morris A. Swertz, Rainer Breitling, Analytical Chemistry, 2011 83 (7), 2786-2793.

See Also

PeakML.Methods.getPhenoData PeakML.Methods.getChromData PeakML.Isotope.getIsotopes

andzajan/mzmatch.R documentation built on Dec. 1, 2020, 11:33 a.m.