PeakML.Isotope.getAbunMtxList: PeakML.Isotope.getAbunMtxList

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

Description

Generates a matrix containing the relative abundance of labelled vs unlabelled isotopes based on the the mean of the peaks in each groups.

Usage

	PeakML.Isotope.getAbunMtxList(isotopeChroms, sampleGroups, useArea)

Arguments

isotopeChroms	The chrom data for isotopes see. PeakML.Isotope.getChromData.
sampleGroups	The sample groups.
useArea	TRUE will sum up all intensities to give area under the curve, FALSE gives maximum intensities.

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.getAbunMtxList returns a matrix containing the relative abundance of labelled vs unlabelled isotopes based on the the mean of the peaks in each groups, replicates along the columns and isotops along the rows.

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

mzmatch.R documentation built on May 31, 2017, 4:31 a.m.