MSnbase: writeMgfData-methods – R documentation

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writeMgfData-methods

Write an experiment or spectrum to an mgf file

Description

Methods writeMgfData write individual "Spectrum" instances of whole "MSnExp" experiments to a file in Mascot Generic Format (mgf) (see http://www.matrixscience.com/help/data_file_help.html for more details). Function readMgfData read spectra from and mgf file and creates an "MSnExp" object.

Arguments

`object`	An instance of class `"Spectrum"` or `"MSnExp"`.
`con`	A valid `connection` or a `character` string with the name of the file to save the object. In case of the latter, a `file` connection is created. If not specified, 'spectrum.mgf' or 'experiment.mgf' are used depending on the class of `object`. Note that existing files are overwritted.
`COM`	Optional character vector with the value for the 'COM' field.
`TITLE`	Optional character vector with the value for the spectrum 'TITLE' field. Not applicable for experiments.

Details

Note that when reading an mgf file, the original order of the spectra is lost. Thus, if the data was originally written to mgf from an MSnExp object using writeMgfData, although the feature names will be identical, the spectra are not as a result of the reordering. See example below.

Methods

signature(object = "MSnExp"): Writes the full exeriment to an mgf file.
signature(object = "Spectrum"): Writes an individual spectrum to an mgf file.

Examples

data(itraqdata)

f <- tempfile()

writeMgfData(itraqdata, con = f)

itraqdata2 <- readMgfData(f)

## note that the order of the spectra and precision of some values
## (precursorMz for instance) are altered
match(signif(precursorMz(itraqdata2),4),
      signif(precursorMz(itraqdata),4))

## [1]  1 10 11 12 13 14 15 16 17 18 ...
## ... but all the precursors are there
all.equal(sort(precursorMz(itraqdata2)),
          sort(precursorMz(itraqdata)),
          check.attributes = FALSE,
          tolerance = 10e-5)

all.equal(as.data.frame(itraqdata2[[1]]),
          as.data.frame(itraqdata[[1]]))

all.equal(as.data.frame(itraqdata2[[3]]),
          as.data.frame(itraqdata[[11]]))

all(featureNames(itraqdata2) == featureNames(itraqdata))

MSnbase

Base Functions and Classes for Mass Spectrometry and Proteomics

v2.16.1

Artistic-2.0

Authors

Laurent Gatto, Johannes Rainer and Sebastian Gibb with contributions from Guangchuang Yu, Samuel Wieczorek, Vasile-Cosmin Lazar, Vladislav Petyuk, Thomas Naake, Richie Cotton, Arne Smits, Martina Fisher, Ludger Goeminne, Adriaan Sticker and Lieven Clement.

Initial release