R: PeakML.Isotope.processUntargettedIsotopes

PeakML.Isotope.processUntargettedIsotopes {mzmatch.R}

R Documentation

PeakML.Isotope.processUntargettedIsotopes

Description

Determines the type of analysis that has to be used to perform the untargetted isotope quantification and parallalizes the process.

Usage

	PeakML.Isotope.processUntargettedIsotopes(peakMLFile, analyse, databases, outDirectory, outFileName, layoutMtx, ppm, stdRTWindow, sampleType,
	sampleNames, peakDataMtx, chromDataList, phenoData, sampleGroups, plotOrder, mzXMLSrc, fillGaps, massCorrection, useArea, filterStringency, baseCorrection, numSlaves, label)

Arguments

`peakMLFile`	The name of the PeakML file which contains the combined peaks of all samples that are filtered, gap filled and identified. See the advanced metabolomics data processing tutorial at http://mzmatch.sourceforge.net/tutorial.mzmatch.r.advanced.html for more information.
`analyse`	Indicates what type of analysis you want to run. The tree possible values at the moment are "identified", "databases" and "allmasses". "identified" and "allmasses" can be used to run an untargetted isotope identification procedure on the given PeakML file looking for all the identified compounds or all masses detected. "databases" can be used to run entire databases such as KEGG and HMDB.
`databases`	A vector containing databases as numbers or strings based on which initial annotations were made or the databases that has to be used for identification. For more information, see 'Identify peaks from data bases' section at http://mzmatch.sourceforge.net/tutorial.mzmatch.r.advanced.php
`outDirectory`	The output directory.
`outFileName`	The output filename
`layoutMtx`	The layout matrix that specifies the layout of the plot to be generated. Leave this as NULL if the number of sample to be plotted is less than or equal to 10. See layout in R more details.
`ppm`	The ppm to specify the mass window for searching the isotopes.
`stdRTWindow`	The standard retention time window. Leave it to NULL if no standard retention time is available for the compound.
`sampleType`	The sample type, eg., negative ionisation.
`sampleNames`	The names of samples.
`peakDataMtx`	The peak data matrix. See PeakML.Methods.getPeakData.
`chromDataList`	The list of chromatograms. See PeakML.Methods.getChromData.
`phenoData`	The phenotype data of the samples. See PeakML.Methods.getPhenoData.
`sampleGroups`	The sample groups.
`plotOrder`	The order in which samples has to be plotted.
`mzXMLSrc`	The path to the raw data mzXML files.
`fillGaps`	"ALLPEAKS" if all the peaks are to gap filled, requied to fill missing signals in some part of the curve. "MISSINGPEAKS", if only the missing peaks have to be filled Or "NONE" if no peaks have to be gap filled. Defaults to "ALLPEAKS".
`massCorrection`	Requied if gap fill is TRUE. This is to correct the natural mass with the ionised mass. See PeakML.Methods.getMassCorrection(). see PeakML.Methods.getMassCorrection.
`useArea`	TRUE if sum of intensities has to be used instead of the maximum of intensities for peak intensity calculations.
`filterStringency`	This is the percentage of samples that needs to be labelled. It can be left to "NULL" if the filter has to be turned off.
`baseCorrection`	TRUE or FALSE based on the requirement of base correction for noisy peaks. Enabling this will make the processing slower.
`numSlaves`	This parameter can be set to indicate the number of CPU cores that can be used for isotope identification and quantification.
`label`	This is the label to be identified. 1 = C13; 2= N15. More will be added as and when implemented.

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.processUntargettedIsotopes generates a pdf document containing the plots of isotopes of each identified compound in the PeakML file specified.

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.