PeakML.Plot.RelatedPeaks {mzmatch.R}R Documentation

PeakML.Plot.RelatedPeaks

Description

Function to generate an overview pdf document containing summary information shown fragment ad other related signals. Peaks shapes and groups annotations. Including putative identifications.

Usage

PeakML.Plot.RelatedPeaks (filename, ionisation="detect", Rawpath=NULL, DBS=dir(paste(find.package("mzmatch.R"), "/dbs", sep=""),full.names=TRUE),outputfile,sampleClasses=NULL)

Arguments

filename

File in peakML format to be used as input file.

ionisation

Ionisation mode of the data set.

Rawpath

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

DBS

Character vector containing names of the compound data bases files in XML format.

outputfile

File name of the pdf output to be created.

sampleClasses

Character vector indicating whihc sample groups should be shown on the plot. If set to NULL all sample groups from the peakML file will be plotted.

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.getGroupAnnotations function allows to access attributes defined in PeakML file.

Value

Plot to the current graphical device.

Author(s)

Andris Jankevics (a.jankevics@rug.nl) Richard Scheltema (r.a.scheltema@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.Read


[Package mzmatch.R version 2.0-6 Index]