Creating an Object

Question

[planetearth]

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

>group1 <- grep("old",rownames([e-mail]))
>group2<- grep("young",rownames([e-mail]))
>cells[group1]
>cells[group2]

What should I use for counts?

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

Thank you.

Answer 1

[Kristoffer Vitting-Seerup]

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.