Select highly variable loci for ATAC-seq

[PeterZZQ]

object <- selectFeatures(object, assay = "RNA")
loci.use <- searchGeneRegions(genes = object@var.features[[1]], species = "mouse")
object@var.features[[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 object@norm.data[[2]][object@var.features[[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.

[sqjin]

@PeterZZQ Please check the function findNearbyLoci.