Problem with Seurat package in PercentageFeatureSet function
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Entering edit mode
6 weeks ago
Yoosef ▴ 60

Hello I encountered a problem when calculating the mitochondrial genome in my samples. This is my code

count <- Read10X("GSM4909254/") #give the name of the folder contains the mentioned files
srobj <- CreateAssayObject(counts = count, project = "GSM4909254", 
                           min.cells = 3, min.features = 200)   #filter the data
head(srobj)


srobj[["MTpercent"]] <- PercentageFeatureSet( srobj, pattern = "^MT-")
srobj$MTpercent

png(filename = "srobj.png", width = 1900,height = 1500,res = 200)
VlnPlot(object = srobj,features = c("nFeature_RNA", "nCount_RNA","MTpercent"),
        ncol = 3,cols = 3,pt.size = 1)
dev. Off()

This is the error I get :

srobj[["MTpercent"]] <- PercentageFeatureSet( srobj, pattern = "^MT-")
Warning: The following arguments are not used: assay
Error in `[.data.frame`(slot(object = x, name = "meta.features"), , i,  : 
  undefined columns selected

and When I try to create a VlnPlot, I only get a white picture and the following warning:

Error in UseMethod(generic = "FetchData", object = object) : 
  no applicable method for 'FetchData' applied to an object of class "Assay"
cell single • 457 views
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1
Entering edit mode

Did you check where the features.tsv.gz file had Gene IDs or Ensembl IDs?

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Thanks a lot for your response. Today, I finally understood what my problem was. I have used CreateAssayObject function, while I should have used CreateSeuratObject. This completely solved my problem.

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1
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Yes, CreateAssayObject function is used for only expression matrix.

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