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wkumler / RaMS

R-based access to Mass-Spectrometry data
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support for UV/DAD data? #10

Closed ethanbass closed 1 year ago

ethanbass commented 2 years ago

Hi,

I was wondering if you would be interested in incorporating support for a function to extract DAD data from mzML files? I have some example files that were converted from the Thermo RAW format using the ThermoRawFileParser that encode both MS and DAD data. I figured out how to extract them using the MzR package, but I think I like you're approach better since it doesn't come with so many dependencies. If you want I could try to throw together a grabMzmlUV function and/or send over some example files.

Thanks!

wkumler commented 2 years ago

Hi Ethan,

I'd be definitely interested in expanding the package functionality to DAD data! I haven't worked with that type of MS at all so if you're able to send some and/or get started on a grab function that'd be welcome. Glad you like the package!

ethanbass commented 2 years ago

I took a first crack at it here: https://github.com/ethanbass/RaMs.

And here is a link to the example files: https://cornell.box.com/v/thermo-mzml1

They were converted from Thermo RAW using the ThermoRawFileParser, as I mentioned before.

I think the solution i came up with is pretty specific to the way DAD data is encoded by Thermo, but I don't have any other example files, so I don't know if (or how) other manufacturers might differ.

I also changed an error to a warning in checkOutputQuality, because I didn't see why the whole function needs to error out if it can't find a certain data type -- like the DAD data for example. It seems like a warning is sufficient here, but feel free to revert if there's something I'm not seeing.

wkumler commented 1 year ago

Closed with #14