PeakML.Read {mzmatch.R}R Documentation

PeakML.Read

Description

This function returns a list containing peak data matrix, list of chromatograms for each peak in the peak data matrix, sample classes, measurement names, mass correction applied to the data set, sample groups, pheno data, corrected retentiontimes, raw retentiontimes, filename and raw data full paths.

Usage

	PeakML.Read(filename, ionisation="detect", Rawpath=NULL)

Arguments

filename

The PeakML file containing peak sets.

ionisation

Defaulted to "detect". See documentation for PeakML.Methods.getProtonCoef.

Rawpath

Path to the raw data if different from the one stored in the PeakML file.

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

R list containing peak data matrix, list of chromatograms for each peak in the peak data matrix, sample classes, measurement names and mass correction applied to the data set.

Author(s)

Achuthanuni Chokkathukalam (unni.chokkathukalam@glasgow.ac.uk) Andris Jankevics (a.jankevics@rug.nl)

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.getMassCorrection, PeakML.Methods.getPeakData, PeakML.Methods.getChromData


[Package mzmatch.R version 2.0-6 Index]