Function not working in Seurat5 because of layers

[MarcElvld]

Dear all,

Working with a merged file of 6 samples in Seurat, as a QC I want to make a list of the genes with the highest read number per cell :
Seu$largest_count <- apply(Seu[['RNA']]@CountS,2, max) #Return per cell highest read number
Seu$largest_index <- apply(Seu[['RNA']]@CountS,2, which.max) #Return rownumber max reads
Seu$largest_gene <- rownames(Seu)[Seu$largest_index] #Return row names of genes with max reads

But in Seurat5 the different samples are stored in different layers. So when I run this code (with the @ replaced by $) I only get numbers from the first layer. How can I make the function to run through the counts of all layers?

Thank you,
Marc

[camilletestard]

Dear all,

I am experiencing the same issue, hopefully bumping up the request! Can we make the "apply" function to run through the counts of all layers?

Thanks!

[wudustan]

You could replace Seu with JoinLayers(Seu)