Question: Classify cells using seurat
gravatar for AB
28 days ago by
United States
AB80 wrote:


I am working on single cell data and I have a general question. Monocle has a function 'classifyCells' to assign celltype using known marker genes. Here is the bit from the documentation

cth <- newCellTypeHierarchy()

MYF5_id <- row.names(subset(fData(cds), gene_short_name == "MYF5"))
ANPEP_id <- row.names(subset(fData(cds), gene_short_name == "ANPEP"))

cth <- addCellType(cth, "Myoblast", classify_func =
    function(x) { x[MYF5_id,] >= 1 })
cth <- addCellType(cth, "Fibroblast", classify_func =
    function(x) { x[MYF5_id,] < 1 & x[ANPEP_id,] > 1 } )

cds <- classifyCells(cds, cth, 0.1)

Is there a similar function is Seurat. Something that allows to classify cells by cell type and adds it to the meta-data in the seurat object?

seurat scrna monocle • 98 views
ADD COMMENTlink written 28 days ago by AB80

I have used SetIdent() to do something like that.

ADD REPLYlink written 27 days ago by Madelaine Gogol4.9k
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