R: Reads mass spectrometry data in mzXML format.

readMzXmlFile {readMzXmlData}

R Documentation

Reads mass spectrometry data in mzXML format.

Description

Reads mass spectrometry data in mzXML format defined in http://tools.proteomecenter.org/mzXMLschema.php.

Usage

readMzXmlFile(mzXmlFile, removeMetaData = FALSE, verbose = FALSE)

Arguments

`mzXmlFile`	`character`, path to mzXML file which should be read.
`removeMetaData`	`logical`, to save memory metadata could be deleted.
`verbose`	`logical`, verbose output?

Value

A list of spectra and metadata.

spectrum$mass: A vector of calculated mass.
spectrum$intensity: A vector of intensity values.
metaData: A list of metaData depending on read spectrum.

Author(s)

Sebastian Gibb mail@sebastiangibb.de

References

Definition of mzXML format: http://tools.proteomecenter.org/mzXMLschema.php

Examples

## load library
library("readMzXmlData")

## get examples directory
exampleDirectory <- system.file("Examples", package="readMzXmlData")

## read example spectrum
spec <- readMzXmlFile(file.path(exampleDirectory, "A1-0_A1.mzXML"))

## print metaData
print(spec$metaData)

## plot spectrum
plot(spec$spectrum$mass, spec$spectrum$intensity, type="l")

[Package readMzXmlData version 2.8.1 Index]