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Implement a readChromData function #286

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jorainer opened this issue Dec 12, 2017 · 1 comment
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Implement a readChromData function #286

jorainer opened this issue Dec 12, 2017 · 1 comment
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@jorainer
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jorainer commented Dec 12, 2017

Implement a readChromData (or readChromatograms) function to read chromatogram data from an mzML file.
This relates to sneumann/mzR#141 in mzR.

@jorainer jorainer self-assigned this Dec 12, 2017
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jorainer commented Dec 13, 2017

@wilsontom and @lgatto, a question: if you run an SRM/MRM experiment and have multiple files (e.g. for multiple samples), you will always have chromatograms for the same ions in each file, right? In other words, the Q1 m/z and the Q3 m/z are supposed to be identical across files. Is the retention time window also expected to be the exact same?

If that's the case, we can use the Chromatograms object to represent a SRM or MRM experiment. The Chromatograms organizes Chromatogram objects in a 2-dimensional array, columns being samples, rows chromatograms for the same m/z value (or m/z value range).

If there is the possibility that two files have chromatograms for completely different (and unrelated) ions (m/z) we have to implement a different object that would be more like the MSnExp that organizes Spectrum objects in one dimension.

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