Reads recursively mass spectrometry data in mzXML format.
Reads recursively all mass spectrometry data in mzXML format in a specified directory.
readMzXmlDir(mzXmlDir, removeCalibrationScans = TRUE, removeMetaData = FALSE, rewriteNames = TRUE, fileExtension = "mzXML", verbose = FALSE)
mzXmlDir |
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removeCalibrationScans |
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removeMetaData |
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rewriteNames |
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fileExtension |
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verbose |
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See readMzXmlFile.
A list of spectra.
[[1]]spectrum$mass: A vector of calculated mass.
[[1]]spectrum$intensity: A vector of intensity values.
[[1]]metaData: A list of metaData depending on read spectrum.
Sebastian Gibb mail@sebastiangibb.de
## load library
library("readMzXmlData")
## get examples directory
exampleDirectory <- system.file("Examples", package="readMzXmlData")
## read example spectra
spec <- readMzXmlDir(exampleDirectory)
## plot spectra
plot(spec[[1]]$spectrum$mass, spec[[1]]$spectrum$intensity, type="n")
l <- length(spec)
legendStr <- character(l)
for (i in seq(along=spec)) {
lines(spec[[i]]$spectrum$mass, spec[[i]]$spectrum$intensity, type="l",
col=rainbow(l)[i])
legendStr[i] <- basename(spec[[i]]$metaData$file)
}
## draw legend
legend(x="topright", legend=legendStr, col=rainbow(l), lwd=1)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.