readMzXmlFile {readMzXmlData}

Reads mass spectrometry data in mzXML format.

Description

Reads mass spectrometry data in mzXML format defined in http://tools.proteomecenter.org/wiki/index.php?title=Formats:mzXML

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 [e-mail]

References

Definition of mzXML format: http://tools.proteomecenter.org/wiki/index.php?title=Formats:mzXML

See Also

readMzXmlDir, importMzXml

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")