PeakML.Isotope.getRatioMtxList: PeakML.Isotope.getRatioMtxList

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

Description

Returns the matrix for each peak group, containing the ratio of labelled vs unlabelled signals for each replicate normalized to one along the columns and isotopes along the columns.

Usage

	PeakML.Isotope.getRatioMtxList(intList, sampleGroups, useArea, metName="")

Arguments

intList	list containing intensities of isotopes.
sampleGroups	The sample groups.
useArea	TRUE will sum up all intensities to give area under the curve, FALSE gives maximum intensities.
metName	name of the metabolite to give the column name of the matrix.

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.getRatioMtxList returns a matrix for each peak group, containing the ratio of labelled vs unlabelled signals for each replicate normalized to one along the columns and isotopes along the columns

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.