Question: Classify cells using seurat
0
gravatar for Apoorva
2.4 years ago by
Apoorva250
United States
Apoorva250 wrote:

Hi,

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 • 2.4k views
ADD COMMENTlink modified 2.1 years ago by dppb0590 • written 2.4 years ago by Apoorva250
1

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

ADD REPLYlink written 2.4 years ago by Madelaine Gogol5.1k
0
gravatar for dppb05
2.1 years ago by
dppb0590
dppb0590 wrote:

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?

There is ClassifyCells function. But keep in mind that this function works differently from monocle::classifyCells. Monocle's docs, as you have probably read, give a good high-level explanation on their classification approach.

For Seurat::ClassifyCells you need some labelled data that will be used to train Random Forest classifiers. Those trained classifiers will then be used to classify your unlabelled data. You could subset your Seurat object (using SubsetData) based on some marker genes and set the ident (using SetIdent) of this subset according to those markers, then use that as your training set.

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by dppb0590
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