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HelenaLC / CATALYST

Cytometry dATa anALYsis Tools
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Merging/combining reclustered clusters into original SCE #338

Closed shanh1 closed 1 year ago

shanh1 commented 1 year ago

Hi there,

Apologies for all the enquiries recently! Thank you for all your support thus far.

I have reclustered one of my clusters from an original SCE object (cluster 19) as it contained naive cells mixed in with other T cells and I wanted to separate it from the main SCE clusters. Upon re clustering, I can see there are sub clusters that are not naive and belong in the original SCE population. Is there any way I can take a subset of the sub clusters and combine them back into the original SCE?

Could I remove cluster 19 from my original SCE (by filterSCE()), recluster and then add the subclusters that are not naive back into the original SCE?

Thank you kindly,

Shan

HelenaLC commented 1 year ago

I am generally happy to help, but if you are struggling with basic R/SingleCellExperiment operations (also issue #337), I suggest you check out some online resources/tutorials to familiarize yourself with manipulating the data structures being used; or/and consulting a bioinformatician for help. GitHub issues are meant for software-related issues/bugs/feature requests, or detailed methodological inquiries, and I have to reserve my time to answer these. Qs regarding subsetting/joining data are usually answered by browsing the web yourself, and can be posted elsewhere if all fails. For what it's worth, you want something like...

sub <- filterSCE(sce1, ...)
sce <- cbind(sce2, sub)