Filter SingleCellExperiment object just by one gene expression
In seurat you use WhichCells but how do you filter/classify your cells based on one gene expression values using SingleCellExperiment object ?
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ZheFrench
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You can treat a SingleCellExperiment just like a standard R data.frame. The columns would allow subsetting on specific cells and the rows would allow subsetting on specific genes.
Here I subset my SingleCellExperiment object sce for only cells that contain the string WT.
sce <- sce[,grep('WT',colnames(sce))]
If you want to filter based on specific gene expression you could do something like this - keeping only cells with over 5k beta-actin reads:
sce <- sce[,which(assay(sce)['ACTB',] > 5000)]
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