Import mgf files as 'MSnExp' instances.
Reads a mgf file and generates an "MSnExp"
object.
readMgfData(filename, pdata = NULL, centroided = TRUE, smoothed = FALSE, verbose = isMSnbaseVerbose(), cache = 1)
filename |
character vector with file name to be read. |
pdata |
an object of class |
smoothed |
|
centroided |
|
cache |
Numeric indicating caching level. Default is 1. Under development. |
verbose |
verbosity flag. |
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.
An instance of
Guangchuang Yu <guangchuangyu@gmail.com> and Laurent Gatto <lg390@cam.ac.uk>
writeMgfData method to write the content of
"Spectrum" or "MSnExp"
objects to mgf files. Raw data files can also be read with the
readMSData function.
data(itraqdata)
writeMgfData(itraqdata, con="itraqdata.mgf", COM="MSnbase itraqdata")
itraqdata2 <- readMgfData("itraqdata.mgf")
## note that the order of the spectra is altered
## and precision of some values (precursorMz for instance)
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
f <- dir(system.file(package="MSnbase",dir="extdata"),
full.name=TRUE,
pattern="test.mgf")
(x <- readMgfData(f))
x[[2]]
precursorMz(x[[2]])
precursorIntensity(x[[2]])
precursorMz(x[[1]])
precursorIntensity(x[[1]]) ## was not in test.mgf
scanIndex(x)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.