[JOSS Review] BUG: `groupFeaturesKPIC2` fails after `findFeaturesXCMS` if `loadRawData = TRUE` about patroon HOT 7 CLOSED

Hi @hechth,

Nearly all of the algorithms implemented or interfaced in patRoon expect centroided data. KPIC2 is one of them, and as far as I am aware XCMS also expects it. Would you be able to re-run it with centroided data?

In the mean while I will clarify this better in the documentation and see if I can add some input data checks to notify the user.

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The commits referenced above add code to verify that MS data is centroided and some additional notes to the documentation.

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I'll check with centroiding the data before whether this works then, thanks for the hints!

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Still failing, now with a different error message on centroided data:

> fGroups <- patRoon::groupFeaturesKPIC2(features)
Verifying if your data is centroided...
Grouping features with KPIC2... Error in rep(0, curdiff) : invalid 'times' argument
In addition: Warning message:
replacing previous import ‘jsonlite::validate’ by ‘shiny::validate’ when loading ‘KPIC’

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Hmm... I am afraid this might be a bug in KPIC2 during RT alignment. If you could share a few MS files that trigger this I could try to take a look what is going on and try add a fix to my fork. I guess if you set rtalign=FALSE to groupFeatures() the error will go away.

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I'll try - I also tried I think finding the features with KPIC but it just seems to be computing forever and gets stuck on 0%.

I can send you more details, but these problems are very likely related to the underlying algorithm, not patRoon itself.

I can play around with it a bit more and create some minimal working example where the error occurs. Thanks for looking into this!

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Yeah, it works with rtalign=FALSE.

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