PeakML.ComparePeakSets {mzmatch.R}R Documentation

PeakML.ComparePeakSets

Description

This function will filter peak sets from one peakml file matching similar peak sets (based on RT and mass window) in the second file.

Usage

PeakML.ComparePeakSets (standard_filename, filename, stdionisation="detect",ionisation="detect", stdRawpath=NULL, Rawpath=NULL, outputfile,ppm=5,rtwin=20,checkIntensity=TRUE,PeakShapeCor=TRUE,PeakShapeCor.thr=0.7)

Arguments

standard_filename

Name ot the standard input file in peakML format.

filename

Name ot the file which has to be processed in peakML format.

stdionisation

Defaulted to "detect". See documentation for PeakML.Methods.getProtonCoef.

ionisation

Defaulted to "detect". See documentation for PeakML.Methods.getProtonCoef.

stdRawpath

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

Rawpath

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

outputfile

Name of the resulting peakML file.

ppm

Mass window to much peak grops in ppm.

rtwin

Retention time window to match peak groups in seconds.

checkIntensity

When is set to TRUE only peak with highes intensity will be selected if more than one peak is matching RT and mass window. This paramater will be ignored if PeakShapeCor is set to true.

PeakShapeCor

Caclulate correlation of peak shape between standards file and matched peaks in input file. Peak with highest signal intensity in peakset is used from both peak sets.

PeakShapeCor.thr

Correlation value threshold which to to retain matched peak sets. If more than one peak sets are matchin criteria, peak with highest correlation value will be kept.

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

List of 3 PeakML data files: matched peak sets, not matched from processed file (file prefix Not_matched) and not matched peak sets from standards file (file prefix STD_not_matched).

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]