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cell type information #2

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BenxiaHu opened this issue May 17, 2021 · 2 comments
Closed

cell type information #2

BenxiaHu opened this issue May 17, 2021 · 2 comments

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@BenxiaHu
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Hello,
when I try to run scDaPars on one public scRNA-seq, I reaslized that I need to provide the cell type information.
scDaPars.res.umap = umap(t(scDaPars.res))
scDaPars.res.umap.data = data.frame(scDaPars.res.umap$layout)
colnames(scDaPars.res.umap.data) = c("Dim1", "Dim2")
scDaPars.res.umap.data$cellType = cell_type$source_name

My question is that scDaPars can identify cell clusters, not depends known cell typ information?
@YiPeng-Gao
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Hello,
when I try to run scDaPars on one public scRNA-seq, I reaslized that I need to provide the cell type information.
scDaPars.res.umap = umap(t(scDaPars.res))
scDaPars.res.umap.data = data.frame(scDaPars.res.umap$layout)
colnames(scDaPars.res.umap.data) = c("Dim1", "Dim2")
scDaPars.res.umap.data$cellType = cell_type$source_name

My question is that scDaPars can identify cell clusters, not depends known cell typ information?

The cell type information is used as ground truth to evaluate if the clustering result is correct. The clustering itself does not require any prior cell type information.

@BenxiaHu
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great.

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@BenxiaHu @YiPeng-Gao