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.
See Also
readMgfData function to read data from and mgf file.
Examples
## Not run:
data(itraqdata)
writeMgfData(itraqdata,file="itraqdata.mgf",COM="MSnbase itraqdata")
itraqdata2 <- readMgfData("itraqdata.mgf")
## 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)
## is TRUE
all.equal(as.data.frame(itraqdata2[[1]]),as.data.frame(itraqdata[[1]]))
## is TRUE
all.equal(as.data.frame(itraqdata2[[3]]),as.data.frame(itraqdata[[11]]))
## is TRUE
## But, beware that
all(featureNames(itraqdata2)==featureNames(itraqdata))
## is TRUE too!
## End(Not run)