Seurat object create

Question

[KOUSTAV]

I need guidance to create Seurat object and how do I understand it properly created. I have to create any new project name for Seurate object ?I did not create any project name so far. How to create new project for Seurat object. Please help.

Seuratobj<-CreateSeuratObject(counts = ctrl_counts,project = Seuratobj,min.cells = 3,min.features = 200) Error in factor(x = project) : object 'Seuratobj' not found

Thank you in advance

[Nitin Narwade]

You can find the description in help page of CreateSeuratObject function

project: Sets the project name for the Seurat object.

so the project is the identifier assigned to your experiment. in your code it should be a string (Ex.: "Cancer scRNA-Seq", "Zebrafish Embryonic Development" etc.) and you specified it without a quote, so R is considering it as an object and not as a string.

code from this tutorial shows an example of how to specify the project for Seurat object

pbmc <- CreateSeuratObject(counts = pbmc.data, project = "pbmc3k", min.cells = 3, min.features = 200)

[KOUSTAV]

Thank you Nitin for your help. Project name here is the main folder generated by cell ranger (name :60 - 502323136).I did not change it. Some output from beginning I have attached here. Could you please give your input to solve the problem.

> Read10X(data.dir ="~/60-502323136/01_Analysis/nacZT0_31032021/raw_feature_bc_matrix")
31053 x 6794880 sparse Matrix of class "dgCMatrix"
   [[ suppressing 34 column names ‘AAACCCAAGAAACACT-1’, ‘AAACCCAAGAAACCAT-1’, ‘AAACCCAAGAAACCCA-1’ ... ]]
   [[ suppressing 34 column names ‘AAACCCAAGAAACACT-1’, ‘AAACCCAAGAAACCAT-1’, ‘AAACCCAAGAAACCCA-1’ ... ]]

Xkr4    . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
Gm1992  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
Gm37381 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
Rp1     . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
Sox17   . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
Gm37323 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
Mrpl15  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
Lypla1  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
Gm37988 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
Tcea1   . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
Rgs20   . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
Gm16041 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
Atp6v1h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
Oprk1   . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
Npbwr1  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......

 ..............................
 ........suppressing 6794846 columns and 31024 rows in show(); maybe adjust 'options(max.print= *, width = *)'
 ..............................
   [[ suppressing 34 column names ‘AAACCCAAGAAACACT-1’, ‘AAACCCAAGAAACCAT-1’, ‘AAACCCAAGAAACCCA-1’ ... ]]

Vmn1r186       . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
AC102264.1     . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
AC125149.3     . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
AC125149.5     . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
AC125149.1     . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
AC125149.2     . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
AC125149.4     . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
AC234645.1     . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
AC168977.2     . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
AC168977.1     . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
AC149090.1     . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
CAAA01118383.1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
Vmn2r122       . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
CAAA01147332.1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
> 
> 
> ctrl_counts <-Read10X(data.dir ="~/60-502323136/01_Analysis/nacZT0_31032021/raw_feature_bc_matrix")
> ctrl <- CreateSeuratObject(counts =  ctrl_counts,min.cells = 3, min.features = 200)
> Seuratobj<-CreateSeuratObject(counts = ctrl_counts,project = Seuratobj,min.cells = 3,min.features = 200)
Error in factor(x = project) : object 'Seuratobj' not found
>  Seuratobj<CreateSeuratObject(Count=ctrl_counts,project = 60-502323136,min.cells=3,min.features=200)
Error: object 'Seuratobj' not found
> 60-502323136<-CreateSeuratObject(Count=ctrl_counts,project = 60-502323136,min.cells=3,min.features=200)
Error in CreateSeuratObject(Count = ctrl_counts, project = 60 - 502323136,  : 
  argument "counts" is missing, with no default

[Nitin Narwade]

Try this,

Seuratobj<-CreateSeuratObject(counts = ctrl_counts,project = "60-502323136",min.cells = 3,min.features = 200)

To save the Seurat object you can use

saveRDS(Seuratobj, "Seuratobj.rds")

This is standard R command and you can get an answer by googling this.

Answer 1

[ATpoint]

The project argument takes a character, so just a name you want to give the project, and as such it must be in quotation marks like "my_project". If you give it a variable then the name must be in the variable. If the variable does not exist then you get this error.

[KOUSTAV]

So, the folder name created by cell ranger is 60 - 502323136. If I want to same Seuratobject in this folder what should be the command?

[KOUSTAV]

Sorry it will be "If I want to Save Seuratobject in this folder what should be the command?"