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sneumann / xcms

This is the git repository matching the Bioconductor package xcms: LC/MS and GC/MS Data Analysis
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Peak mz values when running findChromPeaks on XChromatograms object #765

Closed CLUES-Emory closed 2 months ago

CLUES-Emory commented 2 months ago

Hello, Currently, mz values are dropped when running findChromPeaks on XChromatogram objects, even if the mz range for an XIC is included when defining the XChromatogram option. This is leading to some issues when we are detecting peaks and running correspondence analysis across multiple samples (we are creating XChromatograms from XICs generated in the rawrr package). Is there anyway to include the XChromatogram mz values (and/or the provided range) in the peak tables generated from XChromatograms objects? Thanks!

CLUES-Emory commented 2 months ago

Ah, just realized the feature definitions return the row number of the chromatogram, which allowed me to link back to the original mz and resolves the issue above.

jorainer commented 1 month ago

thanks for reporting! Actually, this is a very interesting issue - indeed, reporting the m/z values in the chromPeaks() matrix if that information is provided/stored in the XChromatograms would be an interesting information.

jorainer commented 1 month ago

btw, with the commit linked above I'm also reporting the chromatogram's m/z in the chromPeaks() matrix.