The readMzXmlData Package

Description

The package reads mass spectrometry data in mzXML format.

Details

Main functions:

readMzXmlFile: Reads mass spectrometry data in mzXML format.

readMzXmlDir: Reads recursively mass spectrometry data in mzXML format in a specific directory.

mqReadMzXml: Reads mass spectrometry data into MALDIquant.

Author(s)

Sebastian Gibb mail@sebastiangibb.de

References

See website: https://strimmerlab.github.io/software/maldiquant/

See Also

readMzXmlDir, readMzXmlFile

Converts XML attributes.

Description

This function converts a XML time attribute to double.

Usage

.attributeTimeToDouble(attributes, attributeName, required = FALSE)

Arguments

Value

double

Author(s)

Sebastian Gibb mail@sebastiangibb.de

See Also

.attributeToString, .attributeToDouble

Converts XML attributes.

Description

This function converts a XML attribute to double.

Usage

.attributeToDouble(attributes, attributeName, required = FALSE)

Arguments

Value

double

Author(s)

Sebastian Gibb mail@sebastiangibb.de

See Also

.attributeToString, .attributeTimeToDouble

Converts XML attributes.

Description

This function converts a XML attribute to character.

Usage

.attributeToString(attributes, attributeName, required = FALSE)

Arguments

Value

character, attribute string

Author(s)

Sebastian Gibb mail@sebastiangibb.de

See Also

.attributeToDouble, .attributeTimeToDouble

Converts base64 character to double.

Description

This function converts a base64 encoded character vector to a double vector.

Usage

.base64decode(
  x,
  size,
  endian = .Platform$endian,
  compressionType = c("none", "gzip")
)

Arguments

Value

Vector of type double.

Author(s)

Sebastian Gibb mail@sebastiangibb.de

See Also

base64decode from base64enc package

Pattern matching.

Description

This function returns double values found in a character.

Usage

.grepDouble(x)

Arguments

Value

double, matched value

Author(s)

Sebastian Gibb mail@sebastiangibb.de

See Also

.grepNumber .grepSubString

Pattern matching.

Description

This function returns numeric values found in a character.

Usage

.grepNumber(x)

Arguments

Value

numeric, matched value

Author(s)

Sebastian Gibb mail@sebastiangibb.de

See Also

.grepDouble .grepSubString

Pattern matching.

Description

This function returns a substring selected by a regular expression.

Usage

.grepSubString(pattern, x)

Arguments

Value

character, matched substring

Author(s)

Sebastian Gibb mail@sebastiangibb.de

See Also

.grepNumber

Parse mzXML files.

Description

This function is defines handlers for XML SAX parser. Internal use only.

Usage

.mzXmlHandlers(fileName, verbose = FALSE)

Arguments

Value

function closure

Author(s)

Sebastian Gibb mail@sebastiangibb.de

References

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

Parse mzXML files.

Description

This function parses mzXML files.

Usage

.parseMzXml(file, verbose = FALSE, ...)

Arguments

Value

Returns a list with metadata and spectra.

Author(s)

Sebastian Gibb mail@sebastiangibb.de

Reads mass spectrometry data in mzXML format.

Description

Internal function.

Usage

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

Arguments

Value

A list of spectra and metadata.

Author(s)

Sebastian Gibb mail@sebastiangibb.de

See Also

readMzXmlFile

Pattern matching.

Description

This function looks for the last match to argument pattern in a file file.

Usage

.revfregexpr(pattern, file)

Arguments

Value

double, position of match.

Author(s)

Sebastian Gibb mail@sebastiangibb.de

Removed functions in package readMzXmlData

Description

These functions are defunct and no longer available.

Details

mqReadMzXml:

use importMzXml instead.

Reads recursively mass spectrometry data in mzXML format.

Description

Reads recursively all mass spectrometry data in mzXML format in a specified directory.

Usage

readMzXmlDir(
  mzXmlDir,
  removeCalibrationScans = TRUE,
  removeMetaData = FALSE,
  rewriteNames = TRUE,
  fileExtension = "mzXML",
  verbose = FALSE
)

Arguments

Details

See readMzXmlFile.

Value

A list of spectra.

• [[1]]spectrum$mass: A vector of calculated mass.

• [[1]]spectrum$intensity: A vector of intensity values.

• [[1]]metaData: A list of metaData depending on read spectrum.

Author(s)

Sebastian Gibb mail@sebastiangibb.de

See Also

readMzXmlFile, importMzXml

Examples

## load library
library("readMzXmlData")

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

## read example spectra
spec <- readMzXmlDir(exampleDirectory)

## plot spectra
plot(spec[[1]]$spectrum$mass, spec[[1]]$spectrum$intensity, type="n")

l <- length(spec)
legendStr <- character(l)
for (i in seq(along=spec)) {
  lines(spec[[i]]$spectrum$mass, spec[[i]]$spectrum$intensity, type="l",
        col=rainbow(l)[i])
  legendStr[i] <- basename(spec[[i]]$metaData$file)
}

## draw legend
legend(x="topright", legend=legendStr, col=rainbow(l), lwd=1)

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

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/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")