Creating an Object
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.
• 1,481 views
•
link
updated
by
Ram
•
written
by
planetearth •
•
written
by
planetearth •
1 answer
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.
• 0 views
•
link
written
by
Kristoffer Vitting-Seerup
Log in to answer this question.
More posts like this
-
normalization in single cell
written by kayah •
-
Cannot convert the inetgarted seurat object to the cds for monocle 3
written by shweta.johari13 •
-
Is my code using Seurat correctly?
written by shweta.johari13 •
-
Filtering genes in scRNA-seq
written by learner-MD •
-
Combine multiple groups on comparison by edgeR
written by camelest •
-
merge two SeuratObjects to do the integration
written by yueli7
-
Subsetting dataset to create 2 seurat objects
written by planetearth •
-
positive and negative Fold Change glmLRT test
written by debitboro
-
Help with linear regression model design
written by mforde84
-
edgeR design matrix gives different results for the same data?
written by cafelumiere12
