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CostaLab / scMEGA

scMEGA: Single-cell Multiomic Enhancer-based Gene regulAtory network inference
https://costalab.github.io/scMEGA
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Use obj.pair to show the expression of marker gene #19

Closed liyang24 closed 1 year ago

liyang24 commented 1 year ago

Hi! I use obj.pair to look at the expression of marker gene. I want to know whether the gene expression matrix in scRNA or the gene score matrix in scATAC is used here ,or the expression quantity after algorithm integration?

obj.pair An object of class Seurat 67334 features across 5396 samples within 2 assays Active assay: RNA (17352 features, 0 variable features) 1 other assay present: ATAC 4 dimensional reductions calculated: pca, umap, harmony, umap_harmony

p <- FeaturePlot(obj.pair, features = c("COL1A1"),reduction ="umap_harmony",min.cutoff = "q10", max.cutoff = "q90")

lzj1769 commented 1 year ago

Hi @liyang24

Here, the gene expression matrix is used.

More specifically, in this object, each cell has two modalities, i.e., RNA and ATAC, generated from the two assays by integration.

So when you visualize the marker genes, the RNA data is used.