writeMgfData-methods.Rd
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.
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.
Optional character vector with the value for the 'COM' field.
Optional character vector with the value for the spectrum 'TITLE' field. Not applicable for experiments.
signature(object = "MSnExp")
Writes the full exeriment to an mgf file.
signature(object = "Spectrum")
Writes an individual spectrum to an mgf file.
readMgfData
function to read data from and mgf file.
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.
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 19 2 20 21 22 23 24 25 26 27 28 29 3 30 31
#> [26] 32 33 34 35 36 37 38 39 4 40 41 42 43 44 45 46 47 48 49 5 50 51 52 53 54
#> [51] 55 6 7 8 9
## [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)
#> [1] TRUE
all.equal(as.data.frame(itraqdata2[[1]]),
as.data.frame(itraqdata[[1]]))
#> [1] TRUE
all.equal(as.data.frame(itraqdata2[[3]]),
as.data.frame(itraqdata[[11]]))
#> [1] TRUE
all(featureNames(itraqdata2) == featureNames(itraqdata))
#> [1] TRUE