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
file <- dir(system.file(package="MSnbase",dir="extdata"),
full.name=TRUE,
pattern="test.mgf")
(x <- readMgfData(file))
x[[2]]
precursorMz(x[[2]])
precursorIntensity(x[[2]])
precursorMz(x[[1]])
precursorIntensity(x[[1]]) ## was not in test.mgf
scanIndex(x)
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