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I am currently working on multiple datasets where each is managed by a separate Seurat object. For each I'd like to also compute the marker genes using the FindAllMarkers function. Where would it be a good practice to save the markers returned from the FindAllMarkers function? I tried adding an extra slot to the Seurat object with no success.

I saw the calc.params slot and though I could add an item to that list. However, it doesn't seem like the right place as that slot is a list of the parameters used for the different functions executed on the data.

Currently I have some wrapping object that has a slot for the Seurat object and a slot for the results from the FindAllMarkers. Is there any better place to put it? Somewhere within the Seurat object?

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  • $\begingroup$ Welcome to the site Gilad. In general it is discouraged to directly access and modify the slots of an object directly. If the object itself doesn't add the information it might be a good reason to not attempt to do it $\endgroup$
    – llrs
    Mar 26 '19 at 10:10
  • $\begingroup$ @llrs - True which is why I'm checking to see if there is any suitable slot that is used for this kind of extensibility. As in the example of calc.params where it is designed in such a way where it is ok to add items to that list $\endgroup$ Mar 26 '19 at 10:15
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You can stash anything you like in the misc slot (present in both v2 and v3 Seurat objects). I often use it for storing marker information to help with organization.

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