Define conditions based on high or low gene expression for scRNAseq analysis

Question

[Abdou-samad]

Hello everyone,

I am a beginner in single cell RNA sequencing analysis. I really need your help. I am wondering how I can group my scRNA data according to high and low gene expression (i.e. HighPD1/LowPD1) and then identify the different cells in the group in both conditions. What I find in most cases are control and treatment conditions, but nothing in the high and low gene expression conditions.

Thank you for your attention.

[Nitin Narwade]

I am not sure whether I understood your question or not but I will try to give some advice based on my understanding.

First you need to extract the expression of gene of interest, then use some expression cut-off and divide the cells into groups based on the selected cut-off.

The provisional code to achieve this in Seurat:

so$marker_exp <- FetchData(so, vars = "geneOfInterest", slot = "data")
so$marker_exp <- if_else(so$marker_exp <= exp_cutoff, "low", "high")

so_high <- subset(so, subset = marker_exp == 'high)
VlnPlot(object = so_high features = 'geneOfInterestToSeeExpression')

Regards,

Nitin N.