View source: R/readWriteMgfData.R
readMgfData | R Documentation |
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)
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