Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Tutorials
Tools
Jobs
Forum
Planet
All »
Home
Log In
Question: Creating an Object
0
gravatar for planetearth
16 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 • 463 views
ADD COMMENT • link •
modified 16 months ago by _r_am ♦ 30k • written 16 months ago by planetearth • 0
1
gravatar for kristoffer.vittingseerup
16 months ago by
kristoffer.vittingseerup • 3.4k
European Union
kristoffer.vittingseerup • 3.4k 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 16 months ago • written 16 months ago by kristoffer.vittingseerup • 3.4k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1665 users visited in the last hour