How to define data directories and syntax before using readMSData in MSnBase
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Last seen 4.9 years ago

Please can someone give me the correct syntax to use to define directories and paths to a directory containing either mzxML or mzML files.

I am trying the following: file <- dir(system.file(package = "MSnbase", dir = "phenolics"),
            full.names = TRUE, pattern = "mzML$")
rawdata <- readMSData(file, msLevel = 1, verbose = FALSE)

​where I have several mzML files in a directory "phenolics" on my C drive.  I get the error saying that at least one function per file needs to be defined. The data was collected using a Waters Synapt G2 and converted using msConvert (gui version) - it contains MS1 and MS2 data as well as lockmass and UV data (4 functions).


I cannot get this to work even if I use mzML files off the web.  Please advise.  Thanks Malcolm Taylor





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