scAI
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Select highly variable loci for ATAC-seq
object <- selectFeatures(object, assay = "RNA")
loci.use <- searchGeneRegions(genes = [email protected][[1]], species = "mouse")
[email protected][[2]] <- loci.use
object <- run_scAI(object, K, do.fast = TRUE, hvg.use1 = TRUE, hvg.use2 = TRUE)
I cannot run through that code for kidney example, Error shows that
Error in [email protected][[2]][[email protected][[2]], ] : invalid or not-yet-implemented 'Matrix' subsetting
loci
seems to be a data frame with 4 columns and the selection requires one region annotation. I think you may miss some function like search_nearby_loci
in MATLAB version.