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Question: Creating an Object
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gravatar for planetearth
19 months ago by
planetearth • 0
planetearth • 0 wrote:

Hi, I'm having trouble with creating objects for each group. Here's what I've done so far

>group1 <- grep("old",rownames(cells@meta.data))
>group2<- grep("young",rownames(cells@meta.data))
>cells[group1]
>cells[group2]

What should I use for counts?

>group1_object <- CreateSeuratObject(counts =    , project = "group1")

Thank you.
R • 571 views
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modified 19 months ago by Ram ♦ 32k • written 19 months ago by planetearth • 0
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gravatar for kristoffer.vittingseerup
19 months ago by
kristoffer.vittingseerup • 3.5k
European Union
kristoffer.vittingseerup • 3.5k wrote:

I would suggest you start by make one Seurat object which you do joint QC and filtering on and a joint clustering (like described in this vignette). To do the sub-clustering you can simply (since you are using Seurat 3 (not Seurat2 or earlier)) use the subset() or the SplitObject() function to respectively subset or create a list with the different Seurat subsets (nice if you subsequently want to do the same analysis to all datasets). You can find example code of how both works here.
ADD COMMENT • link modified 19 months ago • written 19 months ago by kristoffer.vittingseerup • 3.5k
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