<p>You can stash anything you like in the <code>misc</code> slot (present in both v2 and v3 Seurat objects). I often use it for storing marker information to help with organization. </p>

CC BY-SA 4.0
2019-03-26T13:40:41.073Z
2019-03-26T13:40:41.073Z
TimStuart
<p>I am currently working on multiple datasets where each is managed by a separate <code>Seurat</code> object. For each I'd like to also compute the marker genes using the <code>FindAllMarkers</code> function. Where would it be a good practice to save the markers returned from the <code>FindAllMarkers</code> function? I tried adding an extra slot to the <code>Seurat</code> object with no success.</p>

<p>I saw the <code>calc.params</code> 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.</p>

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

CC BY-SA 4.0
2019-03-26T10:10:30.453Z
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
llrs
CC BY-SA 4.0
2019-03-26T10:15:48.510Z
@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
Gilad Green
<seurat>
Storing FindAllMarkers results in Seurat object
# Storing FindAllMarkers results in Seurat object

(Asked by: username_0 on 2019-03-25)

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?

**Tags:** seurat
> **Comments:**
> **username_1**: 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  
> **username_0**: @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  

---

## 1 answers

### Answer by username_2 on 2019-03-26. Score: 3 | Accepted answer

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.


---

