PeakML.Methods.getRawMat: PeakML.Methods.getRawMat

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

Description

This function returns a matrix of peaks from raw LC/MS data file wihing given MZ an RT window.

Usage

	PeakML.Methods.getRawMat(rawfile, scan_start, scan_finis, mz_start, mz_finis, correctedRT, uncorrectedRT)

Arguments

rawfile	R object of the raw data file created from openMSfile () command (mz.R package).
scan_start	Numeric value specifying starting scan from which to read data.
scan_finis	Numeric value specifying end scan from which to read data.
mz_start	Lowest m/z range to be returned.
mz_finis	Highest m/z range to be returned.
correctedRT	Vector of corrected RT values for each measurement scan. If no RT correction was applied raw RT's should be used.
uncorrectedRT	Vector of raw RT values for each measurement scan.

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

Matrix containing 5 clolumns: rawRT, correctedRT, scan_id, mz, intnesity.

Author(s)

Andris Jankevics ([e-mail]) Achuthanuni Chokkathukalam ([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.Read, PeakML.GapFiller, PeakML.xcms.write.SingleMeasurement

andzajan/mzmatch.R documentation built on Dec. 1, 2020, 11:33 a.m.