Help with weighted nearest neighbor analysis

Question

[Chris]

Hi all,

I try to use this vignette on my single cell multiome data and not sure how to get the gene to run the function below. The data from endothelial cell and fibroblast. Would you please have a suggestion? I appreciate your input!

motif.name <- ConvertMotifID(data, name = 'PECAM1')
gene_plot <- FeaturePlot(data, features = "sct_PECAM1", reduction = 'wnn.umap')
motif_plot <- FeaturePlot(data, features = motif.name, min.cutoff = 0, cols = c("lightgrey", "darkred"), reduction = 'wnn.umap')
Error: None of the requested features were found: NA in slot data

https://satijalab.org/seurat/articles/weighted_nearest_neighbor_analysis

Update: the gene from the output of head(topTFs("NK"), 3). No more error now.

[Ram]

What are GENE? and sct_GENE?? Are they placeholders or the actual values you're using?

[Chris]

That just a placeholders because in the vignette, they use actual genes such as TBX21, IRF4, SOX4 with the cell types they have. There genes are regulators for the cell types which I am not sure how to get.

[Ram]

What value are you using?

[Chris]

I use PECAM1, a marker gene for endothelial cell.

[Ram]

And do you see the same error when you use that value? Or is it a different error? Why did you redact the actual gene you're using in the first place?

[Chris]

The error with that value I use, same error. Just because I don't know what gene I should put into the code in this case. I am not sure if it makes sense to put a marker gene of a cell type into the code.

[Ram]

Well, by obfuscating the gene and not mentioning that you did that, you've added room for error. Always provide the exact code you ran and the exact error you faced or we'll end up spending time debugging a different problem.

Please edit your post and make the code and error reflect reality.