PeakML.Write {mzmatch.R}R Documentation

PeakML.Write

Description

This function writes the given peak data to the file specified in the PeakML format. This file format supports the mass traces (features) and the sets-structure utilized by XCMS and as such provides a fully reproducible representation of the contents of an XCMS set structure.

Usage

  PeakML.Write(peakMLdata=NULL, peakDataMtx=NULL, chromDataList=NULL, sampleNames=NULL, rawDataFullPaths=NULL, phenoData=NULL, corRT=NULL, rawRT=NULL, ionisation=NULL, GroupAnnotations=NULL, outFileName)

Arguments

peakMLdata

The list of peak data as provided by the function PeakML.Read. If it is provided all other function arguments beside "outFileName" will be ignored.

peakDataMtx

The peak data matrix as provided by the function PeakML.Read

chromDataList

The list of chromatograms as provided by the function PeakML.Read

sampleNames

The sample names as a character vector.

rawDataFullPaths

Paths to the raw data files as a character vector.

phenoData

The phenotypes as a character vector.

corRT

The corrected retention times as list.

rawRT

The raw retentiontimes as list.

outFileName

The filename for the PeakML file. The path leading up to this file needs to exist, otherwise the function will fail.

ionisation

Character value to be set on to "positive" or "negative" if the mass has to be corrected accordingly, or leave it as "neutral".

GroupAnnotations

List of annotations which should be written to PeakML file. List names should contain annotation names. And each list should contain a vector of the length equal to number of peak groups. NA values should be used if annotation is not present in given group.

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.xcms.write function extends the XCMS package with write functionality for exporting data to other applications. For example, the results of an XCMS step can then be loaded in the user interface environment PeakML Viewer and manipulated there.

Value

This function returns no value, but writes a PeakML file from the the given data.

Author(s)

Achuthanunni 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. In preparation.

See Also

PeakML.Methods.getPeakData


[Package mzmatch.R version 2.0-6 Index]